ISMB 2024
This is a list of all sessions at ISMB 2024.
Filter by days
Filter by session
Filter by speaker
Filter by title
Filter by abstract
Showing 600 talks
| When? | Room | Speaker | Title | Session | Abstract |
|---|---|---|---|---|---|
| 12 July 09:00-09:15 (add to calendar) | 520a | Introduction and Welcome Words | Student Council Symposium | ||
| 12 July 09:15-10:00 (add to calendar) | 520a | Dana Pe'er | Towards plasticity in the tissue context: Characterizing niches | Student Council Symposium | |
| 12 July 10:00-10:15 (add to calendar) | 520a | Sofia Rodriguez | Deep analysis of regulatory networks based on single cell transcriptomics reveals a system of master regulators for Rett syndrome. | Student Council Symposium | Rett syndrome is a mono-chromosomal disorder with a prevalence much higher in women (95% of all cases). This disease is characterized by difficulties [...] |
| 12 July 10:15-10:30 (add to calendar) | 520a | Wisdom A Akurugu | Genetic Determinants of Adrenocorticotropic Hormone Resistance in Children on Corticosteroid Treatment | Student Council Symposium | Inhaled corticosteroids are crucial for managing asthma, but these may cause hypothalamic-pituitary-adrenal suppression (HPAS). Cortisol production is [...] |
| 12 July 10:30-10:45 (add to calendar) | 520a | Ornit Nahman | Cell specific priors rescue differential gene expression in spatial spot-based technologies | Student Council Symposium | Spatial transcriptomics (ST), a breakthrough technology, captures the complex structure and state of tissues. Several ST technologies now exist, most [...] |
| 12 July 10:45-11:05 (add to calendar) | 520a | First Draft Assembly and Annotation of the Genome of the Cadmium-Resistant Fungus Talaromyces santanderensis using Oxford Nanopore sequencing: First Molecular Insights into its Cadmium Resistance. | Student Council Symposium | Contamination of crops soils by cadmium (Cd) is a worldwide threat to ecosystems and human health. High concentrations of Cd damage the cell membrane, [...] | |
| 12 July 10:45-11:05 (add to calendar) | 520a | Constructing representative sequence models for evolutionary analysis of protein superfamilies | Student Council Symposium | The ability to confidently infer evolutionary relationships at the scale of protein superfamilies would profoundly transform biology. While the advent [...] | |
| 12 July 10:45-11:05 (add to calendar) | 520a | Characterization of Non-Equilibrium Phase-Separated Biomolecular Condensates | Student Council Symposium | Biomolecular condensates, such as stress granules (SG), are understood to harbor protein aggregates implicated in neurodegenerative pathologies like A [...] | |
| 12 July 10:45-11:05 (add to calendar) | 520a | Multiomics analysis highlighted the role of senescence in regulating trophoblast differentiation: a promising target for early preeclampsia prediction. | Student Council Symposium | Background: Preeclampsia (PE) is a common gestational disease affecting 2-5% of all pregnancies, with its aetiology associated with defective trophobl [...] | |
| 12 July 11:25-11:40 (add to calendar) | 520a | Iria Pose Lagoa | Unraveling patient heterogeneity through explainable AI and network-based strategies | Student Council Symposium | Complex diseases often present a wide landscape of molecular profiles, posing challenges in identifying biomarkers associated with disease progression [...] |
| 12 July 11:40-11:55 (add to calendar) | 520a | Manoj M Wagle | Interpretable deep generative ensemble learning of cell identity paired with automated annotation for single-cell multi-omics | Student Council Symposium | Single-cell omics technologies, with their recent advancement towards multi-modality, have achieved remarkable success in uncovering cellular heteroge [...] |
| 12 July 11:55-12:10 (add to calendar) | 520a | Miriam Poley-Gil | Exploring the biophysical boundaries of protein families with deep learning methods | Student Council Symposium | Recently, Deep Learning models have revolutionised the Molecular Biology field allowing us to explore the intricate interplay between protein sequence [...] |
| 12 July 12:10-12:15 (add to calendar) | 520a | Utilizing a Novel VAE Pipeline for Tau Inhibitor Screening Validated in Drosophila Melanogaster Alzheimer’s Models | Student Council Symposium | Alzheimer's disease (AD), affecting over 50 million worldwide, is a progressive disorder characterized by Tau protein aggregation, leading to signific [...] | |
| 12 July 12:15-13:00 (add to calendar) | 520a | Keynote: TBD | Student Council Symposium | ||
| 12 July 13:00-14:40 (add to calendar) | 520a | Lunch with Poster Session & Networking | Student Council Symposium | ||
| 12 July 14:55-15:15 (add to calendar) | 520a | FinaleToolkit: Accelerating Cell-Free DNA Fragmentation Analysis with a High-Speed Computational Toolkit | Student Council Symposium | The fragmentation pattern of cell-free DNA (cfDNA) represents a promising non-invasive biomarker for disease diagnosis and prognosis. Numerous fragmen [...] | |
| 12 July 14:55-15:15 (add to calendar) | 520a | Development and Application of the MultiSEp R Package to Identify Multiple Myeloma Achilles' Heels for Drug Discovery | Student Council Symposium | Almost all Multiple Myeloma (MM) patients relapse and ultimately succumb to therapy-resistant disease; there is an urgent need for more effective trea [...] | |
| 12 July 14:55-15:15 (add to calendar) | 520a | Bridging Education and Research: Data Hunters Workshop Empowering Bioinformatics Education via Microbiome Studies | Student Council Symposium | Ensuring access to the bioinformatics field shall be on the agenda of life sciences degrees. This especially applies to biology-related degrees, where [...] | |
| 12 July 14:55-15:15 (add to calendar) | 520a | Seven Domain Topics in Bioinformatics Education - Refining the ISCB Core Competencies to Access Diversity in Training | Student Council Symposium | The ISCB Regional Student Group of Brazil (RSG-Brazil) is at the forefront of promoting bioinformatics and computational biology education in Brazil. [...] | |
| 12 July 15:15-16:30 (add to calendar) | 520a | The impact of Student Council in your personal and scientific trajectory | Student Council Symposium | ||
| 12 July 16:30-17:30 (add to calendar) | 520a | Martin Steinegger | Metagenomic sequence analysis: from protein sequences to structures | Student Council Symposium | In metagenomics, DNA is sequenced directly from the environment, allowing us to study the vast majority of microbes that cannot be cultivated in vitro [...] |
| 12 July 17:30-17:35 (add to calendar) | 520a | Introducing ISCB Student Council activities | Student Council Symposium | ||
| 12 July 17:35-17:55 (add to calendar) | 520a | Closing remarks | Student Council Symposium | ||
| 12 July 17:55-18:00 (add to calendar) | 520a | All on stage for picture/photo of the event | Student Council Symposium | ||
| 12 July 18:30-19:30 (add to calendar) | 517d | Fiona S. L. Brinkman | Sensitive Sustainable Science | Distinguished Keynotes | How do we sustainably maintain and further develop bioinformatics and computational biology (BCB) software, databases and tools, in the face of short [...] |
| 13 July 09:00-10:00 (add to calendar) | 517d | Tandy Warnow | Progress in Large-Scale Phylogenomic Estimation Methods | Distinguished Keynotes | Over the last several years, interest in computing and then using large-scale phylogenies has increased for multiple reasons, including basic science [...] |
| 13 July 10:40-10:50 (add to calendar) | 522 | COSI Opening Remarks | Bio-Ontologies | ||
| 13 July 10:40-11:20 (add to calendar) | 525 | Jennifer Geddes-McAlister | Disruption of ClpX reverses antifungal resistance | CompMS | Fungal disease impacts the lives of almost a billion people across the globe. The opportunistic human fungal pathogen, Cryptococcus neoformans, causes [...] |
| 13 July 10:40-11:20 (add to calendar) | 521 | Rolanda Julius | Expanding data science training and health innovations in Africa: the DS-I Africa Consortium | Education | |
| 13 July 10:40-11:00 (add to calendar) | 520b | Roll Call and Introduction to the Function COSI | Function | Free cash will be given to the 7th and 131st persons to show up. Maybe. [...] | |
| 13 July 10:40-10:45 (add to calendar) | 517d | Welcome | HiTSeq | ||
| 13 July 10:40-11:25 (add to calendar) | 520c | Christopher Quince | Towards fully genome-resolved metagenomics | MICROBIOME | I will discuss the impact of long accurate sequencing reads generated by HiFi PacBio on the assembly of microbial genomes directly from metagenomes. I [...] |
| 13 July 10:40-10:50 (add to calendar) | 520a | Yanli Wang | Opening Remarks | NIH/ODSS | |
| 13 July 10:40-11:20 (add to calendar) | 518 | Carl de Boer | Continual improvement of cis-regulatory models | RegSys | Gene expression is regulated by transcription factors that work together to read cis-regulatory DNA sequences. A primary aim of my group is to deciphe [...] |
| 13 July 10:40-11:00 (add to calendar) | 524c | Shoba Ranganathan | HPC-AI Support for Singapore’s Bioinformaticians and Computational Biologists | Tech Track | NSCC Singapore was established in 2015 as a National Research Infrastructure and manages Singapore’s first national petascale facility with high-perfo [...] |
| 13 July 10:40-10:50 (add to calendar) | 519 | Introduction to iRNA track | iRNA | ||
| 13 July 10:45-11:40 (add to calendar) | 517d | Sushmita Roy | Unsupervised learning approaches for genomics to decipher structure and dynamics of 3D genome organization and gene regulatory networks | HiTSeq | Advances in genomic technologies have substantially expanded our repertoire of high-dimensional datasets that capture different modalities such as the [...] |
| 13 July 10:50-11:55 (add to calendar) | 522 | Mayla Boguslav | Learning from our collective scientific ignorance: How can ontologies help us determine what isn't yet? | Bio-Ontologies | Ontologies beg the question what is or exists (known knowns). I seek to determine what isn't or doesn't exist yet (known unknowns or questions). Ontol [...] |
| 13 July 10:50-11:10 (add to calendar) | 520a | Aisha Montgomery | AI/ML to Identify and Stratify Non-Clinical Factors Contributing to Cancer Health Disparity in Rural Appalachia | NIH/ODSS | Introduction: In the medically underserved area of rural Appalachia, cancer mortality rates are 32% higher than the US average. Social determinants of [...] |
| 13 July 10:50-11:10 (add to calendar) | 520a | Jeremias Sulam | Estimating and Controlling for Fairness in Radiology with Missing Sensitive Information | NIH/ODSS | As the use of machine learning models in real world high-stakes decision settings continues to grow, it is highly important that we are able to audit [...] |
| 13 July 10:50-11:30 (add to calendar) | 519 | SPLASH is a reference-free statistical algorithm, unifying biological discovery in RNA-seq, single cell sequencing and beyond | iRNA | Myriad mechanisms diversify the sequence content of RNA transcripts and are of great interest to single cell biology. Currently, these events are dete [...] | |
| 13 July 11:00-11:40 (add to calendar) | 520b | Valerie de Crécy-Lagard | Linking Gene and function in the post-genomic era: issues and opportunities | Function | Identifying the function of every gene in all sequenced organisms is the major challenge of the post-genomic era and an obligate step for any systems [...] |
| 13 July 11:00-11:20 (add to calendar) | 524c | Robyn Ball | Traversing the mouse-human interface with a knowledge graph of analytic and data services | Tech Track | Functional genomics has generated a wealth of gene regulatory information across species and research has shown that variants can be identified within [...] |
| 13 July 11:10-11:30 (add to calendar) | 520a | Rina Khan | Ethical Development of Imaging Biomarkers for Colorectal Biomarkers | NIH/ODSS | |
| 13 July 11:10-11:30 (add to calendar) | 520a | Deborah Mudali | Examining how social and behavioral determiants affect the prevalence, severity, and outcomes of Long-COVID-19 and health disparity | NIH/ODSS | This research examines how social and behavioral determinants affect the prevalence, severity, and outcomes of Long-COVID-19, and their role in worsen [...] |
| 13 July 11:20-11:40 (add to calendar) | 525 | Martin Frejno | Perception and reality of FDR control, data completeness and quantitative precision in (single-cell proteomics) DIA data | CompMS | Introduction_x000D_ _x000D_ Recently, single cell proteomics (SCP) moved away from TMT labelling and DDA to label-free experiments and DIA due to its [...] |
| 13 July 11:20-11:40 (add to calendar) | 525 | Mathieu Lavallée-Adam | A novel supervised learning algorithm for real-time collision energy selection to optimize peptide fragmentation in mass spectrometry | CompMS | Mass spectrometry is the most popular technique to characterize proteins in complex biological samples. The ability to identify peptides, proteins and [...] |
| 13 July 11:20-11:40 (add to calendar) | 521 | Marta Lloret-Llinares | Expanding the ISCB competency framework to describe professionals in bioinformatics core facilities | Education | The International Society of Computational Biology recently revised its competency framework, which facilitates the design of curricula and profession [...] |
| 13 July 11:20-11:40 (add to calendar) | 518 | Peter Koo | Interpreting Cis-Regulatory Interactions from Large-Scale Deep Neural Networks for Genomics | RegSys | The rise of large-scale, sequence-based deep neural networks (DNNs) for predicting gene expression has introduced challenges in their evaluation and i [...] |
| 13 July 11:20-11:40 (add to calendar) | 524c | Erik Sonnhammer | Network analyses for functional annotation with FunCoup tools | Tech Track | The FunCoup database (https://FunCoup.org) provides comprehensive functional association networks of genes/proteins that were inferred by integrating [...] |
| 13 July 11:25-11:40 (add to calendar) | 520c | Shanfeng Zhu | Effective binning of metagenomic contigs using contrastive multi-view representation learning | MICROBIOME | Contig binning plays a crucial role in metagenomic data analysis by grouping contigs from the same or closely related genomes. However, existing binni [...] |
| 13 July 11:30-11:50 (add to calendar) | 520a | Bankole Olatosi | An Ethical Framework-Guided Tool for Assessing Bias in EHR based Big Data Studies | NIH/ODSS | Background: Current literature describes bias using electronic health records (EHR) for data science research. An important but under-researched ethic [...] |
| 13 July 11:30-11:50 (add to calendar) | 520a | Victor Nwankwo | Modern, Intuitive Tools for Managing AI/ML Data in Health Equity-Focused Multiomic and Population Studies | NIH/ODSS | The evolving use of AI and ML in multiomic and population-wide studies presents researchers with the challenge of managing vast and complex datasets. [...] |
| 13 July 11:30-11:50 (add to calendar) | 519 | Zachary Wakefield | Hybrid exons build genome-wide proteomic complexity | iRNA | Alternative splicing (AS) is a highly regulated process occurring in approximately 95% of encoded proteins, however the global implications on the pro [...] |
| 13 July 11:40-12:00 (add to calendar) | 525 | Varun Ananth | A learned score function improves the power of mass spectrometry database search | CompMS | One of the core problems in the analysis of protein tandem mass spectrometry data is the peptide assignment problem: determining, for each observed sp [...] |
| 13 July 11:40-12:00 (add to calendar) | 521 | Nilson Coimbra | Seven Domain Topics in Bioinformatics Education - Refining the ISCB Core Competencies to Access Diversity in Training | Education | The ISCB Regional Student Group of Brazil (RSG-Brazil) is at the forefront of promoting bioinformatics and computational biology education in Brazil. [...] |
| 13 July 11:40-12:00 (add to calendar) | 520b | Alex Warwick Vesztrocy | Unveiling the Functional Fate of Duplicated Genes Through Expression Profiling | Function | Gene duplication is a major evolutionary source of functional innovation – if one copy maintains the ancestral function then the other is no longer un [...] |
| 13 July 11:40-12:00 (add to calendar) | 517d | Qi Liu | An Adaptive K-Nearest Neighbor Graph Optimized for Single-cell and Spatial Clustering | HiTSeq | Unsupervised clustering is crucial for characterizing cellular heterogeneity in single-cell and spatial transcriptomics analysis. While conventional c [...] |
| 13 July 11:40-12:00 (add to calendar) | 520c | Jim Shaw | Floria: Fast and accurate strain haplotyping in metagenomes | MICROBIOME | Shotgun metagenomics allows for direct analysis of microbial community genetics, but scalable computational methods for the recovery of bacterial stra [...] |
| 13 July 11:40-12:00 (add to calendar) | 518 | Melanie Weilert | Chromatin accessibility is driven by intra-nucleosomal pioneer cooperativity that includes low affinity motifs | RegSys | The regulation of chromatin accessibility at cis-regulatory DNA sequences is a key rate-limiting step for enhancer activation and thus is an important [...] |
| 13 July 11:40-12:20 (add to calendar) | 524c | Rami Mehio | Advances towards comprehensive and accurate whole genome analysis at scale using DRAGEN accelerated algorithms | Tech Track | Research and medical genomics require comprehensive and scalable solutions to drive_x000D_ the discovery of novel disease targets, evolutionary driver [...] |
| 13 July 11:50-12:00 (add to calendar) | 520a | Senait Tekle | Use Explainable AI to Improve the Trust of and Detect the Bias of AI Models | NIH/ODSS | Background: Artificial Intelligence (AI) presents promising advancements to improve healthcare outcomes, yet it also raises new ethical concerns. AI s [...] |
| 13 July 11:50-12:00 (add to calendar) | 519 | Priyanka Sehgal | Splicing-derived neo-epitopes in pediatric high-grade glioma | iRNA | Pediatric high-grade gliomas (pHGG) respond poorly to standard therapies, and the development of novel immunotherapeutics (such as chimeric antigen re [...] |
| 13 July 11:55-12:20 (add to calendar) | 522 | Poster Madness | Bio-Ontologies | Opportunity for poster presenters to give a brief overview of their work and advertise their upcoming poster session [...] | |
| 13 July 12:00-12:20 (add to calendar) | 525 | Matthew Glover | Multi-Omic Data Workflows for Drug Discovery and Development | CompMS | The Centre for Genomics Research (CGR) at AstraZeneca aims to identify and validate novel targets and deliver insights into disease biology by using i [...] |
| 13 July 12:00-12:20 (add to calendar) | 521 | Dusanka Nikolic | Support consistent, competent practice for data science in pathogen genomics: the development of an innovative competency framework | Education | Background: A barrier to the application of pathogen genomics for service delivery is due to a lack of trained healthcare and public health profession [...] |
| 13 July 12:00-12:20 (add to calendar) | 520b | Harsh R. Srivastava | Leveraging deep learning for characterization of malaria parasite PUFs — proteins of unknown function | Function | Exploiting the sequence-structure-function paradigm is crucial for annotating proteins of unknown function (PUFs) in Plasmodium falciparum, a member o [...] |
| 13 July 12:00-12:20 (add to calendar) | 517d | Yuan Gao | Forseti: A mechanistic and predictive model of the splicing status of scRNA-seq reads | HiTSeq | Motivation: Short-read single-cell RNA-sequencing (scRNA-seq) has been used to study cellular heterogeneity, cellular fate, and transcriptional dynami [...] |
| 13 July 12:00-12:20 (add to calendar) | 520c | Mihai Pop | The impact of transitive annotation on the training of taxonomic classifiers | MICROBIOME | A common task in the analysis of microbial communities involves assigning taxonomic labels to the sequences derived from organisms found in the commun [...] |
| 13 July 12:00-12:20 (add to calendar) | 520c | Patrick Bradley | Sensitive, specific association of microbial functions with host phenotypes using Phylogenize2 | MICROBIOME | In metagenomics, a key challenge is to explain differences in microbial communities in terms of gene function. Many common approaches to this problem [...] |
| 13 July 12:00-12:20 (add to calendar) | 520a | Discussion | NIH/ODSS | ||
| 13 July 12:00-12:20 (add to calendar) | 518 | Characterizing transcription factor binding with multi-omics sequence model | RegSys | The linkage between transcription factors (TFs) and cis-regulatory regions (CREs) is crucial to under- standing gene regulation. Conventionally, it is [...] | |
| 13 July 12:00-12:20 (add to calendar) | 518 | Protein Language Models improve the target prediction of nucleic acid-binding proteins | RegSys | Unraveling the DNA and RNA-binding preferences of regulatory proteins, like transcription and splicing factors, is important for understanding gene re [...] | |
| 13 July 12:00-12:20 (add to calendar) | 518 | DNA language models reveal the architecture of nucleotide dependencies in genomes | RegSys | While the genome is composed of individual nucleotides, functional elements such as cis-regulatory elements and structural interactions are formed fro [...] | |
| 13 July 12:00-12:20 (add to calendar) | 518 | LoopHunter: Enhancing Chromatin Loop Annotation by Focusing on Larger Regions in Hi-C Data | RegSys | Chromatin loops, which bring distant loci into close contact, play a crucial role in gene expression and regulation. Although several methods have bee [...] | |
| 13 July 12:00-12:20 (add to calendar) | 518 | A systematic comparison of Machine learning methods for the prediction of enhancer-gene interactions from epigenomic data | RegSys | Understanding the complex interaction between histone modifications, enhancers, and gene regulation is pivotal in deciphering the mechanisms governing [...] | |
| 13 July 12:00-12:20 (add to calendar) | 518 | Q&A for Flash Talks | RegSys | ||
| 13 July 12:00-12:20 (add to calendar) | 519 | Flash talks to advertise the posters | iRNA | A-180 Roni Cohen-Fultheim_x000D_ A-186 Étienne Fafard-Couture_x000D_ A-163 Andrew Tapia_x000D_ A-184 Sumit Tarafder_x000D_ A-157 Ihor Arefiev_x000D_ A [...] | |
| 13 July 12:20-12:40 (add to calendar) | 517d | Computational Advances In Multiomics Analysis Using HiFi Sequencing | HiTSeq | PacBio HiFi sequencing has been used to generate the latest and most complete version of the human genome and has ushered in a new era of bioinformati [...] | |
| 13 July 14:20-15:05 (add to calendar) | 522 | Jiyu Chen | Integration of Background Knowledge for Automatic Detection of Inconsistencies in Gene Ontology Annotation | Bio-Ontologies | Biological background knowledge plays an important role in the manual quality assurance (QA) of biological database records. One such QA task is the d [...] |
| 13 July 14:20-15:00 (add to calendar) | 525 | Jianguo Xia | A unified LC-MS metabolomics framework for multi-omics and systems biology | CompMS | Metabolites are key mediators of host-environment interactions. Global or untargeted metabolomics based on liquid chromatography-mass spectrometry (LC [...] |
| 13 July 14:20-14:40 (add to calendar) | 521 | Sara Fumagalli | Bridging Education and Research: Data Hunters Workshop Empowering Bioinformatics Education via Microbiome Studies | Education | Ensuring access to the bioinformatics field shall be on the agenda of life sciences degrees. This especially applies to biology-related degrees, where [...] |
| 13 July 14:20-15:00 (add to calendar) | 520b | M. Clara De Paolis Kaluza | Crowdsoursing the Fifth Critical Assessment of Protein Function Annotation Algorithms (CAFA 5) | Function | The Critical Assessment of Functional Annotation (CAFA) is a long-standing, ongoing community effort to independently assess computational methods for [...] |
| 13 July 14:20-14:40 (add to calendar) | 517d | Vikram Shivakumar | Sigmoni: classification of nanopore signal with a compressed pangenome index | HiTSeq | Improvements in nanopore sequencing necessitate efficient classification methods, including pre-filtering and adaptive sampling algorithms that enrich [...] |
| 13 July 14:20-14:40 (add to calendar) | 520c | Kristen Curry | Reference-free Structural Variant Detection in Microbiomes via Long-read Co-assembly Graphs | MICROBIOME | Bacterial genome dynamics are vital for understanding the mechanisms underlying microbial adaptation, growth, and their broader impact on host phenoty [...] |
| 13 July 14:20-15:00 (add to calendar) | 520a | Yanbin Yin | Cloud exploration and AI/ML-readiness of CAZyme annotation in human gut microbiome | NIH/ODSS | We developed dbCAN as a software system in 2012 and actively maintain it for automated CAZyme (carbohydrate-active enzymes ) annotation. With an R01 a [...] |
| 13 July 14:20-15:00 (add to calendar) | 520a | Robert Leaman | PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge | NIH/ODSS | PubTator 3.0 (https://www.ncbi.nlm.nih.gov/research/pubtator3/) is an advanced biomedical literature resource featuring search capabilities enabled wi [...] |
| 13 July 14:20-15:00 (add to calendar) | 520a | Trey Saddler | ToxPipe: Harnessing AI and Cloud Computing for Toxicological Data Exploration and Interpretation | NIH/ODSS | ToxPipe is an innovative platform that harnesses expert entrained AI and cloud computing to revolutionize the exploration and interpretation of divers [...] |
| 13 July 14:20-15:00 (add to calendar) | 520a | Discussion | NIH/ODSS | ||
| 13 July 14:20-15:00 (add to calendar) | 518 | Jian Ma | Integrative modeling of multiscale single-cell spatial epigenome | RegSys | Despite significant advancements in high-throughput data acquisition in genomics and cell biology, our understanding of the diverse cell types within [...] |
| 13 July 14:20-14:40 (add to calendar) | 524c | Etai Jacob | Enhancing Clinical Trial Outcomes with AI-based Predictive Biomarker Discovery via Contrastive Learning | Tech Track | Modern clinical trials capture numerous clinicogenomic measurements. Manual discovery of predictive biomarkers is challenging. We introduce a framewor [...] |
| 13 July 14:20-14:40 (add to calendar) | 519 | Qian Shi | Accurate Assembly of Multiple RNA-seq Samples with Aletsch | iRNA | High-throughput RNA sequencing has become indispensable for decoding gene activities, yet the challenge of reconstructing full-length transcripts pers [...] |
| 13 July 14:40-15:00 (add to calendar) | 521 | Nia Hughes | Increasing training access with a new Distributed workshop model | Education | The Canadian Bioinformatics Workshop series (CBW), hosted by Bioinformatics.ca, has provided short-form bioinformatics and computational biology train [...] |
| 13 July 14:40-15:00 (add to calendar) | 517d | Harun Mustafa | Label-guided seed-chain-extend alignment on annotated De Bruijn graphs | HiTSeq | Motivation: Exponential growth in sequencing databases has motivated scalable De Bruijn graph-based (DBG) indexing for searching these data, using ann [...] |
| 13 July 14:40-14:55 (add to calendar) | 520c | Paweł P. Łabaj | Targeted Sequencing and Triplet Loss classification allow for microbiome-based inference of soil sample origin | MICROBIOME | Microbiome characterization has been successfully applied in forensic studies. However, from MetaSUB Consortium and CAMDA we know that the full forens [...] |
| 13 July 14:40-15:00 (add to calendar) | 524c | Gwenn Berry | Miqa: Automating bioinformatics testing, evaluation and validation for real-time performance data & instant bug detection on every code change | Tech Track | Evaluation of bioinformatics pipeline performance (accuracy, robustness, and consistency) is critical both for developing and optimizing top-class alg [...] |
| 13 July 14:40-15:00 (add to calendar) | 519 | Beril Erdogdu | Detecting differential transcript usage in heterogenous populations with SPIT | iRNA | Differential transcript usage (DTU) plays a crucial role in shaping gene expression diversity across different biological scenarios, influencing cellu [...] |
| 13 July 14:55-15:10 (add to calendar) | 520c | Samantha Graham | Integration and analysis of 168,000 human gut microbiome samples | MICROBIOME | The human microbiome, or the collection of microorganisms within the human body, plays an important role in modulating human health and disease. While [...] |
| 13 July 15:00-15:40 (add to calendar) | 525 | Ali Rahnavard | waveome: characterizing temporal dynamics of metabolites in longitudinal studies | CompMS | Longitudinal studies, clinical trials, and omics measurements reshape drug development, providing a comprehensive view of disease progression, treatme [...] |
| 13 July 15:00-15:40 (add to calendar) | 525 | Margaret Martin | AI-driven de novo structural candidate generation for mass spectra annotation | CompMS | Despite the increase in reference library size and available annotation tools, the rate of assignment of molecular structures to mass spectra remains [...] |
| 13 July 15:00-15:40 (add to calendar) | 525 | Yuanye Chi | A consensus serum metabolome by large-scale data mining reveals major gaps in metabolomic measurements and modeling | CompMS | Blood analysis is the most common in biomedical applications and a reference metabolome will be critical for effective annotation and for guiding scie [...] |
| 13 July 15:00-15:40 (add to calendar) | 525 | Gaetan De Waele | Transformers for MALDI-TOF MS-based antimicrobial drug recommendation | CompMS | Timely and effective use of antimicrobial drugs can improve patient outcomes, as well as help safeguard against resistance development. Matrix-assiste [...] |
| 13 July 15:00-15:20 (add to calendar) | 521 | Anna Swan | Learning through play: using games in bioinformatics training | Education | Games are increasingly recognized as effective tools in training to engage participants and facilitate the learning of new concepts. This approach can [...] |
| 13 July 15:00-15:20 (add to calendar) | 520b | Chengxin Zhang | StarFunc: interplaying template-based and deep learning approach for accurate protein function prediction | Function | Despite significant advancements in the development of novel methods for protein function prediction via deep learning, template information often rem [...] |
| 13 July 15:00-15:20 (add to calendar) | 517d | Stephen Hwang | Compressed Indexing for Pangenome Substring Queries | HiTSeq | Pangenomes are growing in number and size, thanks to the prevalence of high-quality long-read assemblies. However, current methods for studying sequen [...] |
| 13 July 15:00-16:00 (add to calendar) | 520a | Toru Shirakawa | Deep LTMLE: Scalable Causal Survival Analysis with Transformer | NIH/ODSS | Causal inference under dynamic interventions from longitudinal data with high dimensional variables such as omics and images which potentially vary ac [...] |
| 13 July 15:00-16:00 (add to calendar) | 520a | Matthew Goodwin | Wearable Biosensing to Predict Imminent Aggressive Behavior in Psychiatric Inpatient Youths with Autism | NIH/ODSS | Aggressive behavior is a prevalent and challenging issue in individuals with autism, especially for those who have limited verbal ability and intellec [...] |
| 13 July 15:00-16:00 (add to calendar) | 520a | Mitzi Morris | Improve speed, scalability, inter-operability of core C++ modules for Stan - a tool doing Bayesian modeling and statistical inference | NIH/ODSS | Software Engineering for Research Software_x000D_ _x000D_ Stan is a tool doing Bayesian modeling and statistical inference. In September 2021, the St [...] |
| 13 July 15:00-16:00 (add to calendar) | 520a | Nomi L Harris | LinkML: A FAIR data modeling framework for the biosciences and beyond | NIH/ODSS | Open science depends on open data. LinkML (Linked data Modeling Language; linkml.io) is an open, extensible modeling framework that makes it easy to m [...] |
| 13 July 15:00-16:00 (add to calendar) | 520a | Nancy Li | Leveraging Language Models for Enhanced Biocuration and User Interaction in Reactome: A Pathway Towards Community-Driven Knowledge Enrichment | NIH/ODSS | The Reactome Pathway Knowledgebase, supported by NIH NHGRI and ODSS, stands as a cornerstone database renowned for its meticulous human curation pract [...] |
| 13 July 15:00-16:00 (add to calendar) | 520a | Discussion | NIH/ODSS | ||
| 13 July 15:00-15:20 (add to calendar) | 518 | William Noble | Enhancing Hi-C contact matrices for loop detection with Capricorn, a multi-view diffusion model | RegSys | Motivation: High-resolution Hi-C contact matrices reveal the detailed three-dimensional architecture of the genome, but high-coverage experimental Hi- [...] |
| 13 July 15:00-15:20 (add to calendar) | 524c | Aurélien Luciani | UniProt: The Universal Protein resource: new features, access and tools for protein data | Tech Track | The Universal Protein resource – UniProt – after its more than 20 years of existence, is now a_x000D_ fundamental component in the bioinformatics and [...] |
| 13 July 15:00-15:30 (add to calendar) | 519 | Ana Victoria Conesa Cegarra | Bias analysis for long-reads transcriptomics multi-sample datasets | iRNA | Long-read sequencing technologies such as PacBio and Oxford Nanopore are reshaping transcriptomics. The enhanced precision and depth of sequencing fro [...] |
| 13 July 15:00-15:30 (add to calendar) | 519 | Yu-Jen Lin | RISE: Relative Impact of Splicing and Expression in RNA-seq studies | iRNA | RNA-seq has been widely used to quantify expression and splicing changes in transcriptomes. Although biological consequences arise from changes in bot [...] |
| 13 July 15:00-15:30 (add to calendar) | 519 | Eraj Khokhar | From Noise to Signal: Quantifying Stochasticity in mRNA Splicing | iRNA | Splicing is likely a major contributor to noise in mRNA regulation, with errors in splicing leading to reduced transcriptional efficiency and wasted t [...] |
| 13 July 15:05-15:30 (add to calendar) | 522 | Michael Bradshaw | The cyclic nature of biases against understudied genes and diseases in knowledge graph embedding link prediction models | Bio-Ontologies | Knowledge graph embedding (KGE) models have been successfully used for a variety of biomedical applications, but have yet to be effectively applied to [...] |
| 13 July 15:10-15:30 (add to calendar) | 520c | Ananthan Nambiar | MC-Funcformer: A foundational model of microbial community metabolism | MICROBIOME | Microbial communities are remarkably complex and encompass an incredible diversity of bacteria, archaea, fungi, and viruses. The metabolic functions o [...] |
| 13 July 15:10-15:30 (add to calendar) | 520c | Serghei Mangul | Assessing Microbial Genome Representation Across Various Reference Databases: A Comprehensive Evaluation | MICROBIOME | Metagenomics research can provide significant insights into the composition, diversity and functions of mixed microbial communities found in various e [...] |
| 13 July 15:20-15:40 (add to calendar) | 521 | Priyanka Surana | Empowering Global Genomic Innovation: The BioDev Network's Educational Blueprint for Cutting-Edge Science and Inclusion | Education | The Biodata Developers' (BioDev) Network is committed to advancing open-access genomic and life science discovery globally through strategic education [...] |
| 13 July 15:20-15:40 (add to calendar) | 520b | Alexander Chervov | ProtBoost: Prediction of functional properties of the proteins by Py-Boost and protein language models (CAFA5 top2) | Function | We will describe machine learning approach to predict protein functions based on their sequences - which allowed our team to win CAFA5 top 2 position [...] |
| 13 July 15:20-15:40 (add to calendar) | 517d | Hugo Magalhães | Sequence-to-graph alignment based copy number calling using a flow network formulation | HiTSeq | Variation of copy number (CN) between individuals has been associated with phenotypic differences. Consequently, CN calling is an important step for d [...] |
| 13 July 15:20-15:40 (add to calendar) | 518 | Gabriel Dolsten | Ultra-long-range and interchromosomal loops link T cell superenhancers | RegSys | Functional enhancer-promoter interactions are typically thought to occur at distances less than two megabases. To explore the role of long-range regul [...] |
| 13 July 15:30-15:55 (add to calendar) | 522 | Azza Althagafi | Prioritizing Causative Genomic Variants by Integrating Molecular and Functional Annotations from Multiple Biomedical Ontologies | Bio-Ontologies | Whole-exome and genome sequencing are widely used for diagnosing_x000D_ patients with rare diseases, but many remain undiagnosed due to_x000D_ undisco [...] |
| 13 July 15:30-16:00 (add to calendar) | 520c | Victor Gordeev | A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater | MICROBIOME | Wastewater genomic surveillance of SARS-CoV-2 has emerged as a scalable, cost-effective, passive surveillance tool to monitor viral variants circulati [...] |
| 13 July 15:30-16:00 (add to calendar) | 520c | Nitesh Kumar Sharma | MetaViz: Realistic assortment of novel metagenomics benchmarks with diverse biological and technological characteristics | MICROBIOME | Metagenomics research relies heavily on bioinformatics methods for analyzing complex microbial communities, necessitating rigorous validation through [...] |
| 13 July 15:30-16:00 (add to calendar) | 520c | Jonas Grove | Phage Host Prediction Using Novel Global-Scale Phage-Host Interaction Atlas and Genomic Language Models | MICROBIOME | Viruses, including bacteriophages and archaeal viruses, are the most abundant form of life on earth (1031), interacting with all life and shaping the [...] |
| 13 July 15:30-15:50 (add to calendar) | 519 | Teresa Rummel | Deciphering Transcriptional Bursting Using Single-Cell Metabolic Labeling Data | iRNA | In single cells, transcription is governed by bursts. The kinetics of transcriptional bursting are defined by the burst frequency, describing how ofte [...] |
| 13 July 15:40-16:00 (add to calendar) | 525 | Martin Frejno | The sky is the limit: a cloud-based proteomics platform for the masses | CompMS | Background: Laboratories dealing with bottom-up proteomics data often encounter computational hurdles in the journey from raw data to conclusive insig [...] |
| 13 July 15:40-16:00 (add to calendar) | 521 | Report from New York City: Bioinformatics Education Summit 2024 | Education | This session will provide a summary of topics covered at the Bioinformatics Education Summit (BES), an annual international gathering of the bioinform [...] | |
| 13 July 15:40-16:00 (add to calendar) | 520b | Huiying Yan | GORetriever: Reranking protein-description-based GO candidates by literature-driven deep information retrieval for precise protein function annotation | Function | The vast majority of proteins still lack experimentally validated functional annotations, which highlights the importance of developing high-performan [...] |
| 13 July 15:40-16:00 (add to calendar) | 517d | Timofey Prodanov | Targeted genotyping of complex polymorphic genes using short and long reads | HiTSeq | The human genome contains numerous highly polymorphic loci, rich in tandem repeats and structural variants. There, read alignments are often ambiguous [...] |
| 13 July 15:40-16:00 (add to calendar) | 518 | Ghulam Murtaza | scGrapHiC: Deep learning-based graph deconvolution for Hi-C using single cell gene expression | RegSys | Single-cell Hi-C (scHi-C) protocol helps identify cell-type-specific chromatin interactions and sheds light on cell differentiation and disease progre [...] |
| 13 July 15:40-16:00 (add to calendar) | 524c | TBD | Tech Track | TBD [...] | |
| 13 July 15:50-16:00 (add to calendar) | 519 | Pavel Sumazin | Coordinated regulation by lncRNAs results in tight lncRNA-target couplings | iRNA | The characterization of long noncoding RNA (lncRNA) function is a major challenge in RNA biology with applications to basic, translational, and medica [...] |
| 13 July 16:40-17:05 (add to calendar) | 522 | Emily Bordeleau | Taking AIIM at antibiotic resistance: harmonizing the nomenclature for aminoglycoside inactivating enzymes | Bio-Ontologies | Multidrug-resistant pathogens continue to challenge aminoglycoside antibiotics with the spread of genetic elements encoding aminoglycoside modifying e [...] |
| 13 July 16:40-17:00 (add to calendar) | 525 | Haixu Tang | SpecEncoder: Deep Metric Learning for Accurate Peptide Identification in Proteomics | CompMS | Tandem mass spectrometry (MS/MS) is a crucial technology for large-scale proteomic analysis. The protein database search or the spectral library searc [...] |
| 13 July 16:40-17:00 (add to calendar) | 521 | Pavlin G. Poličar | Teaching Bioinformatics through the Analysis of SARS-CoV-2: Project-Based Training for Computer Science Students | Education | We learn more effectively through experience and reflection than through passive reception of information. Bioinformatics offers an excellent opportun [...] |
| 13 July 16:40-17:00 (add to calendar) | 520b | Quancheng Liu | InterLabelGO+: Unraveling label correlations in protein function prediction | Function | Accurate prediction of protein functions is crucial for understanding biological processes and advancing biomedical research. However, the rapid growt [...] |
| 13 July 16:40-17:00 (add to calendar) | 517d | Varuni Sarwal | VISTA: An integrated framework for structural variant discovery | HiTSeq | Structural variation (SV), refers to insertions, deletions, inversions, and duplications in human genomes. With advances in whole genome sequencing (W [...] |
| 13 July 16:40-17:00 (add to calendar) | 520c | Yanni Sun | Towards more accurate microbial source tracking via non-negative matrix factorization (NMF) | MICROBIOME | Motivation: The microbiome of a sampled habitat often consists of microbial communities from various sources, including potential contaminants. Microb [...] |
| 13 July 16:40-17:00 (add to calendar) | 520a | Luciano Nocera | Multi-Context Graph Neural Networks for Enhanced Multivariate Time-Series Analysis in Healthcare | NIH/ODSS | Effective multivariate time-series (MTS) analysis in healthcare is crucial for various medical tasks and requires capturing complex inter-variable rel [...] |
| 13 July 16:40-17:00 (add to calendar) | 520a | Yasin Khadem Charvadeh | Clustering-Informed Shared-Structure Variational Autoencoder for Missing Data Imputation in Large-Scale Healthcare Data | NIH/ODSS | Despite advancements in managing healthcare data, missing data challenges persist in Electronic Health Records (EHR) and patient-reported health data, [...] |
| 13 July 16:40-17:00 (add to calendar) | 518 | Emily Maciejewski | Cross-species and tissue imputation of species-level DNA methylation samples across mammalian species | RegSys | DNA methylation data offers valuable insights into various aspects of mammalian biology. However, the availability of such data for many mammals has b [...] |
| 13 July 16:40-17:00 (add to calendar) | 519 | Stefan Prodic | SWARM: Single-molecule Workflow for Analysing RNA Modifications | iRNA | The epitranscriptome contains over 170 chemical modifications that play a pivotal role in regulating RNA properties and function across various RNA cl [...] |
| 13 July 17:00-17:40 (add to calendar) | 525 | Kyowon Jeong | FLASHTagger: An open-source web application for ion type- and precursor mass-free protein identification in top-down mass spectrometry | CompMS | The growing capacity to detect proteins and protein complexes in MS pose computational challenges in identifying them through Top-DownMS (TDMS). While [...] |
| 13 July 17:00-17:40 (add to calendar) | 525 | Lincoln Harris | Imputation of cancer proteomics data with a deep model that learns jointly from many datasets | CompMS | TMT proteomics suffers from excessive missing values, especially in the large-scale, multi-batch experimental setting. Imputation is an analytical sol [...] |
| 13 July 17:00-17:40 (add to calendar) | 525 | Husen M. Umer | Proteogenomics analysis of human tissues using pangenomes | CompMS | The genomics landscape is evolving with the emergence of pangenomes, challenging the conventional single-reference genome model. The new human pangeno [...] |
| 13 July 17:00-17:40 (add to calendar) | 525 | Cecile Le Sueur | Optimising Thermal Proteome Profiling experimental design with GPMelt | CompMS | Thermal proteome profiling (TPP) combines cellular thermal shift assay and quantitative mass spectrometry to explore protein interactions and states p [...] |
| 13 July 17:00-17:20 (add to calendar) | 521 | Nelly Sélem-Mojica | Closing the computational biology “knowledge gap”: Spanish Wikipedia as a case study | Education | Motivation: Wikipedia is a vital open educational resource in computational biology. The quality of computational biology coverage in English Wikipedi [...] |
| 13 July 17:00-17:20 (add to calendar) | 520b | Joel Roca Martinez | Discovery of PETases using a computational classification system | Function | Plastic accumulation is a pressing environmental issue that has escalated in recent decades. With around 25 million tons produced yearly, polyethylene [...] |
| 13 July 17:00-18:00 (add to calendar) | 517d | Long-read sequencing and pangenome perspective of structural variation | HiTSeq | ||
| 13 July 17:00-17:15 (add to calendar) | 520c | Yanbin Yin | Carbohydrate-active enzyme annotation in microbiomes using dbCAN3 | MICROBIOME | Carbohydrate active enzymes (CAZymes) are made by various organisms for complex carbohydrate metabolism. Genome mining of CAZymes has become a routine [...] |
| 13 July 17:00-17:20 (add to calendar) | 520a | Ansaf Salleb-Aouissi | SCH: Predicting and Preventing Adverse Pregnancy Outcomes in Nulliparous Women | NIH/ODSS | Adverse pregnancy outcomes (APOs), including preterm birth (PTB) and preeclampsia (PE), have been exceedingly challenging problems in obstetrics, pred [...] |
| 13 July 17:00-17:20 (add to calendar) | 520a | Juexin Wang | SCH: Graph-based Spatial Transcriptomics Computational Methods in Kidney Diseases | NIH/ODSS | _x000D_ [...] |
| 13 July 17:00-17:20 (add to calendar) | 518 | Mirae Kim | Ontology-aware prediction of tissue-specific DNA methylation | RegSys | DNA methylation (DNAm) has shown tremendous potential in distinguishing physiological states such as aging and cancer progression, and epigenetic cloc [...] |
| 13 July 17:00-17:20 (add to calendar) | 519 | Fatima Mostefai | Refinement of SARS-CoV-2 Intra-host Mutations Using Explainable Representations | iRNA | SARS-CoV-2, an RNA virus, has evolved into multiple variants by accumulating mutations during transmission (inter-host) and infection (intra-host). De [...] |
| 13 July 17:05-17:30 (add to calendar) | 522 | Hande McGinty | Investigating Food Composition Components in Cancer Prevention and Therapy using Knowledge Graphs | Bio-Ontologies | Flavonoids are polyphenolic compounds found in plants and naturally occur in fruits, vegetables, teas, wines, and chocolate. Flavonoids also have know [...] |
| 13 July 17:15-17:30 (add to calendar) | 520c | Adrian Martin-Segura | NUTRIclock, NEURAL NETWORKS ANALYSIS OF MICROBIOME FOR IMPLEMENTING PRECISSION NUTRITION IN AGING. | MICROBIOME | Aging is the greatest risk factor for the development of chronic diseases like neurodegenerative disorders or cancer. The increase in life expectancy [...] |
| 13 July 17:20-18:00 (add to calendar) | 521 | Francis Ouellette | Celebrating 25 Years of Bioinformatics.ca | Education | Over the past 25 years, Bioinformatics.ca has been at the forefront of bioinformatics education in Canada. Initially launched as a series of introduct [...] |
| 13 July 17:20-17:40 (add to calendar) | 520b | David Medina-Ortiz | Plastic-Ml-Tool, a machine learning tool for discovering and optimising plastic degrading enzymes | Function | Plastic contamination is a significant environmental threat that negatively impacts habitats, species, and ecosystems. Recycling strategies can involv [...] |
| 13 July 17:20-17:40 (add to calendar) | 520a | Bengie L Ortiz | AI/ML Ready mHealth and Wearable Data for Dyadic HCT | NIH/ODSS | Hematopoietic cell transplantation (HCT) is a potent form of immunotherapy_x000D_ for high risk blood diseases. Given the high risk associated with HC [...] |
| 13 July 17:20-17:40 (add to calendar) | 520a | Alex Wagner | Enhancing the AI-readiness of gnomAD with GA4GH Genomic Knowledge Standards | NIH/ODSS | The clinical interpretation of genomes is a labor-intensive process that remains a barrier to scalable genomic medicine. Efforts to improve this “inte [...] |
| 13 July 17:20-18:00 (add to calendar) | 518 | Michael Hoffman | Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome | RegSys | We will discuss a new method, Virtual ChIP-seq, which predicts binding of individual transcription factors in new cell types using an artificial neura [...] |
| 13 July 17:20-18:00 (add to calendar) | 519 | Ashley Laughney | Tackling the genotype-to-phenotype problem in cancer evolution | iRNA | Predicting protein function from sequence, also known as genotype-to-phenotype mapping, remains a central challenge in biology. This is because most p [...] |
| 13 July 17:30-18:00 (add to calendar) | 522 | COSI Day 1 Wrap-up | Bio-Ontologies | Wrap-up and open time for questions [...] | |
| 13 July 17:30-17:40 (add to calendar) | 520c | Yifan Jiang | MIOSTONE: Modeling microbiome-trait associations with taxonomy-adaptive neural networks | MICROBIOME | The human microbiome, a complex ecosystem of microorganisms inhabiting the body, plays a critical role in human health. Investigating its association [...] |
| 13 July 17:40-18:00 (add to calendar) | 525 | Shantanu Jain | An algorithm for decoy-free false discovery rate estimation in XL-MS/MS | CompMS | Motivation: Cross-linking tandem mass spectrometry (XL-MS/MS) proteomics is an established technique that determines distance constraints between resi [...] |
| 13 July 17:40-18:00 (add to calendar) | 520b | Yang Lu | A BLAST from the past: revisiting BLAST's E-value | Function | The Basic Local Alignment Search Tool, BLAST, is an indispensable tool for genomic research._x000D_ BLAST established itself as the canonical tool for [...] |
| 13 July 17:40-18:00 (add to calendar) | 520c | Alice McHardy | Critical Assessment of Metagenome Interpretation - Updates and Future Benchmarking Challenges | MICROBIOME | |
| 13 July 17:40-18:00 (add to calendar) | 520a | Vida Abedi | Enhancing Imputation for Clinical Research: The Path for a Flexible Toolkit | NIH/ODSS | Background: Missing data in clinical research restricts robust analysis and AI/ML model training. This project addresses this challenge by presenting [...] |
| 13 July 17:40-18:00 (add to calendar) | 520a | Closing Remarks | NIH/ODSS | ||
| 14 July 09:00-10:00 (add to calendar) | 517d | Guillaume Bourque | Human genome 2.0 : why a pangenome graph is better for genetic and epigenetic analyses | Distinguished Keynotes | Genomic analyses often start by mapping reads to a reference genome. But, in every individual, there are DNA variants and sequences that are unique to [...] |
| 14 July 10:40-10:50 (add to calendar) | 522 | COSI Announcements | Bio-Ontologies | ||
| 14 July 10:40-11:15 (add to calendar) | 525 | Swapnil Sawant | Building a Future-Proof Resource: The Comprehensive Modernization of TAIR | BioInfo-Core | Since its inception in 1999, The Arabidopsis Information Resource (TAIR) has been an essential global resource for plant biologists, offering curated [...] |
| 14 July 10:40-11:40 (add to calendar) | 521 | When Visualization Meets AI: Exploring Opportunities | BioVis | Visualization and AI are increasingly intertwined. AI is being employed to enhance visualization design and to simplify interaction with data. Meanwhi [...] | |
| 14 July 10:40-11:20 (add to calendar) | 520a | Laura Arbour | The Silent Genomes Project: Building the path to equitable genomic care for Indigenous patients, one variant at a time. | Bioinformatics in Canada | There is broad concern that genomic technologies may not reach those with the greatest health disparities. There are numerous reasons why there are ba [...] |
| 14 July 10:40-11:20 (add to calendar) | 520b | Rafael Najmanovich | Fast, high-performance biophysics-based computational methods in function prediction | Function | In this presentation I will discuss a number of computational methods that rely o a simple approximation to molecular interactions to being proportion [...] |
| 14 July 10:40-11:40 (add to calendar) | 517d | Why and how long reads are used to improve gene isoform quantification | HiTSeq | ||
| 14 July 10:40-11:25 (add to calendar) | 520c | Susannah Tringe | Sequence-based interrogation of soil microbiomes and their ecosystem benefits | MICROBIOME | Plants roots and the soil they grow in are heavily colonized with microbes that play critical roles in nutrient cycling and transport as well as influ [...] |
| 14 July 10:40-11:20 (add to calendar) | 518 | Maria Colomé Tatché | Single-cell and single-molecule computational epigenomics | RegSys | Recent breakthroughs in high-throughput sequencing of single cells are revolutionizing the biological and biomedical sector. Among the different -omic [...] |
| 14 July 10:40-11:20 (add to calendar) | 524ab | Richard Scheuermann | Combining computational pipelines and text mining to build a cell type knowledge graph resource | Text Mining | Advances in sequencing technologies are now allowing for the comprehensive analysis of whole genome structure (epigenomic) and expression (transcripto [...] |
| 14 July 10:40-10:50 (add to calendar) | 524c | Philippe Youkharibache | Introduction: "Visualizing Protein Function from Genes to Biology: Back to the Future" | Visualizing Protein Function from Genes to Biology: Back to the Future | Molecular graphics has been in development for 60 years through the emergence of innovative research and computer technologies one after the other tha [...] |
| 14 July 10:40-11:20 (add to calendar) | 519 | Christopher Burge | Interpretable models to understand regulation of RNA splicing | iRNA | We are developing fully interpretable models of RNA splicing and its regulation for improved understanding and various applications. We recently descr [...] |
| 14 July 10:50-11:55 (add to calendar) | 522 | Karin Slater | Exploring Multiple Perspectives for Associative Knowledgebases | Bio-Ontologies | Databases encoding associative relationships between biomedical entities function as background knowledge which are leveraged for a range of purposes. [...] |
| 14 July 10:50-11:20 (add to calendar) | 524c | Barry Honig | Predicting Protein-Protein Interactions | Visualizing Protein Function from Genes to Biology: Back to the Future | The PrePPI algorithm is unique in its ability to predict whether and how two proteins interact on a proteomic scale. PrePPI considers all 200 million [...] |
| 14 July 11:15-12:20 (add to calendar) | 525 | AI and LLMs in cores: How are we using them now? | BioInfo-Core | A panel discussion around the adoption and use of LLMs and AI within bioinformatics core facilities or similar settings. What works, what doesn't? Pra [...] | |
| 14 July 11:20-11:40 (add to calendar) | 520a | Beatriz Lujan Toro | From Sequences to Reports: A Controlled Approach to Pipeline Validation in Cancer Genomics | Bioinformatics in Canada | The Genomics program at the Ontario Institute for Cancer Research (OICR) specializes in providing genome sequencing and analysis services, offering wh [...] |
| 14 July 11:20-11:40 (add to calendar) | 520b | R. Gonzalo Parra | Energetic Local Frustration Through Time and Species | Function | According to the Principle of Minimal Frustration, folded proteins minimize the amount of strong energetic conflicts in their native states. However, [...] |
| 14 July 11:20-11:40 (add to calendar) | 518 | Yang Yang | REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data | RegSys | Motivation: Profiling of gene expression and chromatin accessibility by single-cell multi-omics approaches can help to systematically decipher how tra [...] |
| 14 July 11:20-11:40 (add to calendar) | 524ab | Arvind Mer | Enhancing Machine Learning Based Drug Response Prediction Models via Text Mining-Driven Feature Selection Approach | Text Mining | Predicting anticancer treatment responses from baseline genomic data is a formidable challenge in personalized cancer medicine. Machine learning is in [...] |
| 14 July 11:20-11:40 (add to calendar) | 524ab | Maaly Nassar | Streamlining Drug Development with Conversational AI-Powered Knowledge Graphs: From Preclinical Discovery to Clinical Trials | Text Mining | The drug development industry faces an efficacy crisis, with a 90% clinical trial failure rate, an average of 9 years, and $1.5 billion spent on bring [...] |
| 14 July 11:20-11:50 (add to calendar) | 524c | John Moult | Critical assessment in Computational Structural Biology | Visualizing Protein Function from Genes to Biology: Back to the Future | As science evolves, the old ways of ensuring rigor, particularly the venerable peer-reviewed journal paper system, are breaking down. On the other han [...] |
| 14 July 11:20-11:40 (add to calendar) | 519 | Ruian Shi | IsoCLR: Contrastive learning for RNA foundation models | iRNA | In the face of rapidly accumulating genomic data, our understanding of the RNA regulatory code remains incomplete. Recent self-supervised methods in o [...] |
| 14 July 11:25-11:40 (add to calendar) | 520c | Luis Pedro Coelho | Understanding the small proteins from the global microbiome | MICROBIOME | Small proteins, crucial across all life domains, have been overlooked in large-scale microbiome studies due to limitations in both wet lab and bioinfo [...] |
| 14 July 11:40-12:00 (add to calendar) | 521 | Zeynep H. Gümüş | PRIMAVO: Precision Immune Monitoring Assay Visualization Online | BioVis | Cancer immunotherapies are revolutionizing clinical practice, yet only a fraction of patients derive clinical benefit, and some experience adverse eve [...] |
| 14 July 11:40-12:00 (add to calendar) | 520a | Erika Frangione | The Canadian Genomic Data Commons (CGDC): A Platform for National Genomic Data Sharing | Bioinformatics in Canada | Background: Clinical data generated from genome sequencing (GS) is an ever-growing and valuable resource. To date however, this data has been largely [...] |
| 14 July 11:40-12:00 (add to calendar) | 520b | Mahta Mehdiabadi | Function Prediction of Intrinsically Disordered Proteins and Regions: A Graph Auto-Encoder Approach | Function | Intrinsically disordered proteins/regions (IDPs/IDRs) lack a well-defined three-dimensional structure yet carry out essential biological functions. Du [...] |
| 14 July 11:40-12:00 (add to calendar) | 517d | Sudhanva Shyam Kamath | Telomere-to-telomere assembly by preserving contained reads | HiTSeq | Automated telomere-to-telomere (T2T) de novo assembly of diploid and polyploid genomes remains a formidable task. A string graph is a commonly used as [...] |
| 14 July 11:40-11:55 (add to calendar) | 520c | James Morton | Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles | MICROBIOME | Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by heterogeneous cognitive, behavioral and communication impairments. Di [...] |
| 14 July 11:40-12:00 (add to calendar) | 518 | Reetika Ghag | scHOCMO: Higher Order Correlation Model for Single-cell Multi-omics | RegSys | Single-cell technologies enable system level interrogations across several molecular layers at a single-cell resolution. Current single-cell technolog [...] |
| 14 July 11:40-12:00 (add to calendar) | 524ab | Cathy Wu | eMIND: Enabling automatic collection of protein variation impacts in Alzheimer’s disease from the literature | Text Mining | Alzheimer’s disease and related dementias (AD/ADRDs) are among the most common forms of dementia, and yet no effective treatments have been developed. [...] |
| 14 July 11:40-12:00 (add to calendar) | 519 | Uwe Ohler | Explaining Deep Neural Networks for the Prediction of Translation Initiation | iRNA | Regulation of mRNA translation enables rapid and local control of gene expression. As rate-limiting step, translation initiation is primarily controll [...] |
| 14 July 11:50-12:10 (add to calendar) | 524c | Jianlin Cheng | Protein Structure Accuracy Estimation Using Geometry-Complete Graph Neural Networks | Visualizing Protein Function from Genes to Biology: Back to the Future | Estimating the accuracy of protein structural models is a critical task in protein bioinformatics. The need for robust methods in the estimation of pr [...] |
| 14 July 11:55-12:20 (add to calendar) | 522 | Matthew Cannon | Extracting Clinical Significance for Drug-Gene Interactions using FDA Label Packages | Bio-Ontologies | The drug-gene interaction database (DGIdb) is a resource that aggregates interaction data from over 40 different resources into one platform with the [...] |
| 14 July 11:55-12:10 (add to calendar) | 520c | Xiaofang Jiang | Metagenomic Mining Reveals Niche-Specific Bilirubin Reductases in the Gut Microbiome | MICROBIOME | The gut microbiome plays crucial roles in animal health and metabolism, including the biotransformation of host and diet-derived metabolites. The micr [...] |
| 14 July 12:00-12:20 (add to calendar) | 521 | Eric Mörth | The Best of Both Worlds: Blending Mixed Reality and 2D displays in an Hybrid Approach for Visual analysis of 3D Tissue Maps | BioVis | We introduce a novel hybrid system that combines a Mixed Reality (MR) stereoscopic view of 3D spatial data with linked views on a conventional 2D disp [...] |
| 14 July 12:00-12:20 (add to calendar) | 520a | Abdul Rahman Diab | Binomify: Unified normalization of ChIP-seq data through negative binomial regression | Bioinformatics in Canada | ChIP-seq data is crucial for understanding the mechanisms of gene regulation, and there is a need for a statistically-principled normalization method [...] |
| 14 July 12:00-12:20 (add to calendar) | 520b | Yaron Orenstein | Mapping the affinity of protein-protein interactions with multiple amino acid mutations using deep neural networks | Function | Protein-protein interactions (PPIs) play vital roles in diverse biological processes. Hence, measuring PPIs is critical for decoding the evolution of [...] |
| 14 July 12:00-12:20 (add to calendar) | 517d | Can Firtina | Rawsamble: Overlapping and Assembling Raw Nanopore Signals using a Hash-based Seeding Mechanism | HiTSeq | Although raw nanopore signal mapping to a reference genome is widely studied to achieve highly accurate and fast mapping of raw signals, mapping to a [...] |
| 14 July 12:00-12:20 (add to calendar) | 518 | Pan-cell type continuous chromatin state annotation of all IHEC epigenomes | RegSys | Understanding the mechanistic basis of genetic disease requires annotating the regulatory elements in the human genome. To this end, international con [...] | |
| 14 July 12:00-12:20 (add to calendar) | 518 | Automated and genome-scale exploration of the cis-regulatory code involved in neuronal differentiation | RegSys | Gene expression is controlled by proximal and distal cis-regulatory elements (CREs), containing DNA motifs bound by various transcription factors (TFs [...] | |
| 14 July 12:00-12:20 (add to calendar) | 518 | Expanding GTEx dataset with brain ontology-based graph neural networks to investigate genetic impacts on brain diseases | RegSys | The human brain, with its intricate network of diverse regions, profoundly influences disease development. The Genotype-Tissue Expression (GTEx) progr [...] | |
| 14 July 12:00-12:20 (add to calendar) | 518 | Interpretable single-cell factor decomposition using sciRED | RegSys | Single-cell RNA sequencing (scRNA-seq) enables the exploration of gene expression heterogeneity within large cell populations, arising from biological [...] | |
| 14 July 12:00-12:20 (add to calendar) | 518 | Accurate allocation of multi-mapped reads enables regulatory element analysis at repeats | RegSys | Transposable elements (TEs) and other repetitive regions have been shown to contain gene regulatory elements, including transcription factor binding s [...] | |
| 14 July 12:00-12:20 (add to calendar) | 518 | Q&A for Flash Talks | RegSys | ||
| 14 July 12:00-12:20 (add to calendar) | 524ab | Poster Flash Presentations | Text Mining | ||
| 14 July 12:00-12:20 (add to calendar) | 519 | Can Cenik | Translational efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes | iRNA | Characterization of shared patterns of RNA expression between genes across conditions has led to the discovery of novel biological functions and regul [...] |
| 14 July 12:10-12:20 (add to calendar) | 524c | Ravi Abrol | The NSF Funded iCn3D POSE Project for Collaborative Research and Education in Mechanistic Biology | Visualizing Protein Function from Genes to Biology: Back to the Future | iCn3D is an interactive web-based software for studying molecules in biology. It helps visualize and analyze 3-dimensional (3D) models of molecules li [...] |
| 14 July 14:20-15:05 (add to calendar) | 522 | Fernando Zhapa-Camacho | Predicting protein functions using positive-unlabeled ranking with ontology-based priors | Bio-Ontologies | Automated protein function prediction is a crucial and widely studied problem in bioinformatics. Computationally, protein function is a multilabel cla [...] |
| 14 July 14:20-14:50 (add to calendar) | 525 | Francesco Lescai | Streamlining Bioinformatics Pipelines with Nextflow: A Scalable, Portable, Reproducible, and Collaborative Solution. | BioInfo-Core | Bioinformatics cores face significant challenges, especially when running pipelines across multiple computing environments, including portability, sca [...] |
| 14 July 14:20-15:20 (add to calendar) | 521 | Sehi L'Yi | Understanding Visualization Authoring for Genomics Data through User Interviews | BioVis | Genomics experts use data visualization to extract and share insights from complex and large-scale data sets. The complexity of genomics data analysis [...] |
| 14 July 14:20-15:20 (add to calendar) | 521 | Suzanne Paley | New BioCyc Visualization Tools for Genome Exploration and Comparison | BioVis | We introduce two new BioCyc visualization tools for exploring genomes, with the goal of accelerating science by helping users to rapidly navigate and [...] |
| 14 July 14:20-15:20 (add to calendar) | 521 | Yannis Nevers | Matreex: compact and interactive visualisation of large gene families | BioVis | Studying gene family evolution strongly benefits from insightful visualisations. However, the ever-growing number of sequenced genomes is leading to i [...] |
| 14 July 14:20-15:20 (add to calendar) | 521 | Hiruna Samarakoon | Interactive visualisation of raw nanopore signal data with Squigualiser | BioVis | Nanopore sequencing measures ionic current during the translocation of DNA, RNA or protein molecules through a nanoscale protein pore. This raw curren [...] |
| 14 July 14:20-15:20 (add to calendar) | 521 | Devin Lange | Aggregate Annotated Single-Cell Heatmap Visualizations | BioVis | Heatmaps are commonly used in the biomedical field to visualize tabular data. In the single-cell domain, heatmaps are frequently used to visualize cel [...] |
| 14 July 14:20-15:00 (add to calendar) | 520a | Abdoulaye Diallo | Bioinformatics and AI for precision farming | Bioinformatics in Canada | Precision agriculture/farming is becoming the main approach to tackle the food needs for the increasing population in the world. Sustainable agricultu [...] |
| 14 July 14:20-14:40 (add to calendar) | 520b | Vishal Joshi | Utilising Large Language Models for GO Term Extraction in UniProt Annotation | Function | Automatic Annotation(AA) objective_x000D_ Manually reviewed records (UniProtKB/SwissProt) constitute only about 0.23% of UniProtKB; expert curation is [...] |
| 14 July 14:20-14:40 (add to calendar) | 517d | Igor Martayan | Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets | HiTSeq | In this paper, we introduce the Conway-Bromage-Lyndon (CBL) structure, a compressed, dynamic and exact method for_x000D_ representing k-mer sets. Orig [...] |
| 14 July 14:20-14:40 (add to calendar) | 520c | Christina Boucher | Scalable de novo Classification of Antimicrobial Resistance of Mycobacterium Tuberculosis | MICROBIOME | We develop a robust machine learning classifier using both linear and nonlinear models (i.e., LASSO logistic regression (LR) and random forests (RF)) [...] |
| 14 July 14:20-14:40 (add to calendar) | 518 | Hirak Sarkar | A count-based model for delineating cell-cell interactions in spatial transcriptomics data | RegSys | Motivation: Cell-cell interactions (CCIs) consist of cells exchanging signals with themselves and neighboring cells by expressing ligand and receptor [...] |
| 14 July 14:20-15:00 (add to calendar) | 524ab | Peipei Ping | An informatic path to better understanding of cardiovascular biology and medicine | Text Mining | We will present an overview on our bioinformatics platforms as well as our use cases applying text mining approaches to better understand cardiovascul [...] |
| 14 July 14:20-14:35 (add to calendar) | 524c | Aron Marchler-Bauer | The impact of comparative structure analysis on protein classification at NCBI | Visualizing Protein Function from Genes to Biology: Back to the Future | NCBI's Conserved Domain Database was developed with the goal of increasing the coverage and specificity of protein family model-based genome annotatio [...] |
| 14 July 14:20-14:40 (add to calendar) | 519 | Yaron Orenstein | CellRBP: Improving Protein-RNA Binding Prediction In Vivo Using Cell-Type-Specific Features | iRNA | RNA-binding proteins play important roles in various cellular processes. For this reason, researchers have developed experimental assays to measure pr [...] |
| 14 July 14:35-14:50 (add to calendar) | 524c | Chris Henn | From Immersive Visualization to Interdisciplinary Communication | Visualizing Protein Function from Genes to Biology: Back to the Future | |
| 14 July 14:40-15:00 (add to calendar) | 520b | Weining Lin | ProstGOPred: Advancing Protein Function Prediction through Graph Contrastive Learning and Structure-Aware Protein Language Model Embeddings | Function | We introduce ProstGOPred, a state-of-the-art protein function prediction model that integrates both protein sequence and structural information with e [...] |
| 14 July 14:40-15:00 (add to calendar) | 517d | Xin Yuan | Learning Locality-Sensitive Bucketing Functions | HiTSeq | Many tasks in sequence analysis ask to identify biologically related sequences in a large set. Edit distance is widely used in these tasks as a measur [...] |
| 14 July 14:40-15:00 (add to calendar) | 520c | Youping Deng | Genomic analysis reveals dysregulation of the intratumor microbiome related to immune response in lung cancer | MICROBIOME | Background: Identifying factors underlying resistance to immune checkpoint therapy (ICT) is still challenging. Intratumor microbes (bacteria, fungi, a [...] |
| 14 July 14:40-15:00 (add to calendar) | 520c | Jithin Sunny | Bioinformatics exploration of bacterial communities and plastic-degrading laccase from the gut microbiomes of plastic degrading beetle larvae | MICROBIOME | This study utilizes comprehensive bioinformatics approaches to investigate the gut bacterial population of mealworms and superworms and to mine for en [...] |
| 14 July 14:40-15:00 (add to calendar) | 518 | Xinhai Pan | Mapping lineage-resolved scRNA-seq data with spatial transcriptomics using TemSOMap | RegSys | Spatial transcriptomics (ST) has become a powerful technique that bridges the gap between traditional gene expression analysis and spatial information [...] |
| 14 July 14:40-15:00 (add to calendar) | 519 | Kaitlin Laverty | Reconstructing the sequence specificities of RNA-binding proteins across eukaryotes | iRNA | RNA-binding proteins (RBPs) are key regulators of gene expression. Here, we introduce RBPzoo — a resource of RNAcompete-derived in vitro RNA-binding d [...] |
| 14 July 14:50-15:10 (add to calendar) | 525 | Nikhil Kumar | Leveraging the NF-Core Framework for sharable institutional Nextflow modules at Memorial Sloan Kettering Cancer Center | BioInfo-Core | Four 10 minute talks about different aspects of pipelines within the context of core facilities or related settings:_x000D_ _x000D_ Nikhil Kumar (nikh [...] |
| 14 July 14:50-15:10 (add to calendar) | 525 | Leshkowitz Dena | UTAP2: User-friendly Transcriptome and Epigenome Analysis Pipeline | BioInfo-Core | UTAP2 empowers researchers to unlock the mysteries of gene expression and epigenetic modifications with ease. This user-friendly, open-source pipeline [...] |
| 14 July 14:50-15:00 (add to calendar) | 524c | Marcus De Almeida Mendes | Visualizing Immune Epitope Data: The Innovations of IEDB-3D 2.0 | Visualizing Protein Function from Genes to Biology: Back to the Future | |
| 14 July 15:00-15:20 (add to calendar) | 520a | Pierre-Étienne Jacques | UseGalaxy Canada now in production | Bioinformatics in Canada | We are pleased to announce the release of the UseGalaxy Canada initiative (https://starthere.usegalaxy.ca). In collaboration with the international co [...] |
| 14 July 15:00-15:20 (add to calendar) | 520b | Mengzhou Hu | Evaluation of large language models for discovery of gene set function | Function | Gene set analysis is a mainstay of functional genomics, but it relies on curated databases of gene functions that are incomplete. Here we evaluate fiv [...] |
| 14 July 15:00-15:20 (add to calendar) | 517d | Kayvon Mazooji | Fast Multiple Sequence Alignment via Multi-Armed Bandits | HiTSeq | Multiple sequence alignment is an important problem in computational biology with applications that include phylogeny and the detection of remote homo [...] |
| 14 July 15:00-15:20 (add to calendar) | 518 | Rian Pratama | Enhancing spatial transcriptomics analysis using deep learning-based batch effect mitigation | RegSys | Spatial transcriptomics (ST) is a groundbreaking technique for studying the correlation between cellular organization within a tissue and their physio [...] |
| 14 July 15:00-15:20 (add to calendar) | 524ab | Inge Holtman | The Netherlands Neurogenetics Database: Reveiling clinical, neuropathological and genetic heterogeneity of brain-disorders | Text Mining | The brain is susceptible to a wide-range of neurodegenerative disorders, that share pathophysiological mechanisms, genetic risk factors, and are frequ [...] |
| 14 July 15:00-15:20 (add to calendar) | 524ab | Zhiyong Lu | GeneAgent: Self-verification Language Agent for Gene Set Knowledge Discovery | Text Mining | Genomics has been a research interest of molecular biologists for a long time. Recent studies have shown promising results by harnessing the instructi [...] |
| 14 July 15:00-15:10 (add to calendar) | 524c | Sandra Porter | New iCn3D tools for educators: color keys and collections | Visualizing Protein Function from Genes to Biology: Back to the Future | Molecular modeling programs, such as iCn3D, are increasingly being used in the classroom. Enhancements to accessibility and usability are contributing [...] |
| 14 July 15:00-15:10 (add to calendar) | 519 | Shaimae Elhajjajy | A novel NLP-based RBP binding motif and context discovery method using multiple-instance learning | iRNA | RNA-binding proteins (RBPs) are the primary mediators of mRNA regulation, dynamically governing complex processes such as splicing, cleavage, and degr [...] |
| 14 July 15:05-15:30 (add to calendar) | 522 | An Phan | Protein Function: how much do we know and how much do we care? | Bio-Ontologies | The resources required to study gene function are limited, especially when considering the number of genes in the human genome and the complexity of t [...] |
| 14 July 15:10-15:30 (add to calendar) | 525 | Grace Pigeau | Managing Big Data in a High-Throughput Genomics Pipeline | BioInfo-Core | The Genome Sequence Informatics (GSI) team at OICR handled the analysis and processing of over 1.2 petabytes of data in 2023. The resources required t [...] |
| 14 July 15:10-15:30 (add to calendar) | 525 | George Bell | Novel Linux-style code helps us all down the road | BioInfo-Core | Python, Matlab, and especially R -- all have code bases that can help you go far. But for biologists who can't program, asking them to try can lea [...] |
| 14 July 15:10-15:20 (add to calendar) | 520c | NetBio Opening | NetBio | ||
| 14 July 15:10-15:25 (add to calendar) | 524c | Jiyao Wang | iCn3D: visualization, analysis & sharing of protein structures and interactions | Visualizing Protein Function from Genes to Biology: Back to the Future | It’s challenging to understand 3D structural data. To address this, the web-based iCn3D (I-see-in-3D) viewer uses all kinds of 3D, 2D, and 1D views to [...] |
| 14 July 15:10-15:30 (add to calendar) | 519 | Kristina Sungeun Song | snoFlake: Discovery of a snoRNA-guided splicing regulatory complex via the snoRNA-RBP interactome | iRNA | Box C/D small nucleolar RNAs (snoRNAs) are noncoding RNAs crucial for guiding 2’-O-ribose methylation in ribosomal RNA during ribosome biogenesis, pri [...] |
| 14 July 15:20-15:40 (add to calendar) | 521 | Devin Lange | Aardvark: Composite Visualizations of Trees, Time-Series, and Images | BioVis | How do cancer cells grow, divide, proliferate and die? How do drugs influence these processes? These are difficult questions that we can attempt to an [...] |
| 14 July 15:20-15:40 (add to calendar) | 520a | Deshan Perera | Apollo: A comprehensive GPU-powered Within-host Viral simulator with tissue and cellular hierarchies for studying viral evolutionary and infection dynamics. | Bioinformatics in Canada | The advent of high-throughput sequencing technologies coupled with breakthroughs in third-generation sequencing has allowed new exploration into withi [...] |
| 14 July 15:20-15:40 (add to calendar) | 520b | Dana Varghese | Transformer based data mining for predicting moonlighting in proteins and comparison with first principle annotation | Function | Moonlighting proteins are a specific group of multifunctional proteins that independently carry out distinct functions at various time points, under d [...] |
| 14 July 15:20-15:40 (add to calendar) | 517d | Seong Woo Han | Contrasting and Combining Transcriptome Complexity Captured by Short and Long RNA Sequencing Reads | HiTSeq | High-throughput short-read RNA sequencing has given researchers unprecedented detection and quantification capabilities of splicing variations across [...] |
| 14 July 15:20-16:00 (add to calendar) | 520c | Sergio Baranzini | Towards semantic representation and causal inference in biomedicine. Challenges and applications | NetBio | Massive amounts of data and information are available for analysis in biomedicine. However, integration of these resources in a powerful statistical b [...] |
| 14 July 15:20-15:40 (add to calendar) | 518 | Zhana Duren | Gene Regulatory Networks analysis from single cell multi-omics data | RegSys | Existing methods for gene regulatory networks (GRN) inference rely on gene expression data alone or on lower resolution bulk data. Despite the recent [...] |
| 14 July 15:20-15:40 (add to calendar) | 524ab | Andrew Tran | MolLM: A Unified Language Model for Integrating Biomedical Text with 2D and 3D Molecular Representations | Text Mining | The current paradigm of deep learning models for the joint representation of molecules and text primarily relies on 1D or 2D molecular formats, neglec [...] |
| 14 July 15:25-15:40 (add to calendar) | 524c | Henry Jakubowski | Using iCn3D to address molecular structure/function and to bridge the biology and chemistry educational communities | Visualizing Protein Function from Genes to Biology: Back to the Future | Molecular structures determine the properties and functions of molecules throughout chemistry, biology, and their integrated disciplines, yet the lack [...] |
| 14 July 15:30-15:55 (add to calendar) | 522 | Brook Santangelo | Harmonizing human and microbial datasets to explore mechanisms of the gut microbiome in disease | Bio-Ontologies | The integration of disparate forms of biological data is essential for understanding human health and disease. Doing so is particularly challenging in [...] |
| 14 July 15:30-15:40 (add to calendar) | 519 | Ruiyan Hou | scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3' scRNA-seq data | iRNA | Three-prime single-cell RNA-seq (scRNA-seq) has been widely employed to profile cellular transcriptomes, however, its power of analysing polyadenylati [...] |
| 14 July 15:40-16:00 (add to calendar) | 521 | Komlan Atitey | Boosting Data Interpretation with GIBOOST to Enhance Visualization of High-Dimensional Data | BioVis | Effective visualization of current biomedical data from high-throughput technologies is essential for proper interpretability of complex biological pr [...] |
| 14 July 15:40-16:00 (add to calendar) | 520a | J Maxwell Douglas | Utanos: A general-purpose shallow whole genome sequencing analysis toolkit identifies interpretable copy number signatures | Bioinformatics in Canada | Whole genome sequencing (WGS) is a powerful method for monitoring mutations in cancer genomes. However, the deep sequencing needed in a traditional WG [...] |
| 14 July 15:40-16:00 (add to calendar) | 520b | Asaf Salamov | Gene families of unknown function conserved across Fungi | Function | We constructed conserved gene families from over 2000 fungal genomes using MMseqs2 clustering algorithm, which included 339 gene clusters, encompassin [...] |
| 14 July 15:40-16:00 (add to calendar) | 517d | Sergii Strelchuk | Quantum Computing for Genomic Analysis | HiTSeq | Many essential tasks in genomic analysis are extremely difficult for classical computers due to problems inherently hard to solve efficiently with cla [...] |
| 14 July 15:40-16:00 (add to calendar) | 518 | Maggie Beheler-Amass | Dynamic Gene Regulatory Network Inference with Interpretable, Biophysically-Motivated Neural ODEs | RegSys | Gene Regulatory Networks (GRNs) are complex dynamical systems that modulate gene expression and drive transitions between phenotypic cell states. Dete [...] |
| 14 July 15:40-16:00 (add to calendar) | 524ab | Xiangru Tang | BioCoder: A Benchmark for Bioinformatics Code Generation with Large Language Models | Text Mining | Pre-trained large language models have significantly improved code generation. As these models scale up, there is an increasing need for the output to [...] |
| 14 July 15:40-15:50 (add to calendar) | 524c | Jose Duarte | RCSB.org: a one-stop shop to explore biology in 3D | Visualizing Protein Function from Genes to Biology: Back to the Future | We will present the latest developments from the RCSB Protein Data Bank organization in relation to its main web portal RCSB.org. The portal now integ [...] |
| 14 July 15:40-16:00 (add to calendar) | 519 | Farica Zhuang | G4mer: Transcriptome-wide prediction of RNA G-quadruplexes with a deep RNA language model | iRNA | RNA G-quadruplexes (rG4) are RNA secondary structures known to play an important role in gene regulation. Despite their importance, the effects of gen [...] |
| 14 July 15:50-16:00 (add to calendar) | 524c | Marcelo Querino Lima Afonso | Advancing Molecular Graphics: MolviewSpec and Recent Enhancements in Molstar | Visualizing Protein Function from Genes to Biology: Back to the Future | |
| 14 July 16:40-17:05 (add to calendar) | 522 | Alex Clark | Using ontologies to make bioassay protocols machine readable | Bio-Ontologies | Bioassay protocols have lagged other areas of drug discovery in terms of digitization. While molecules and proteins have spawned entire disciplines (c [...] |
| 14 July 16:40-17:10 (add to calendar) | 525 | Short Talks, Various topics | BioInfo-Core | Patricia Carvajal-López (pati@ebi.ac.uk) - Competency framework profiles to reflect career progression within bioinformatics core facility scientists_ [...] | |
| 14 July 16:40-17:00 (add to calendar) | 521 | Xiaocheng Zeng | Unveil Cis-acting Combinatorial mRNA Motifs by Interpreting Deep Neural Network | BioVis | Cis-acting mRNA elements play a key role in the regulation of mRNA stability and translation efficiency. Revealing the interactions of these elements [...] |
| 14 July 16:40-17:20 (add to calendar) | 520a | Vincent Ferretti | The Quebec Genomic Data Center | Bioinformatics in Canada | The Quebec Genomic Data Center (CQDG), launched in April 2024, is a collaborative research infrastructure project whose mission is to enable the devel [...] |
| 14 July 16:40-17:00 (add to calendar) | 520b | Jun-Tao Guo | Improved prediction of DNA and RNA binding proteins with deep learning models | Function | Nucleic acid-binding proteins (NABPs), including DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs), play important roles in essential biolog [...] |
| 14 July 16:40-17:00 (add to calendar) | 517d | Franziska Görtler | Adaptive Digital Tissue Deconvolution | HiTSeq | Motivation: The inference of cellular compositions from bulk and spatial transcriptomics data increasingly complements data analyses. Multiple computa [...] |
| 14 July 16:40-17:00 (add to calendar) | 520c | Kevin Rupp | Modeling metastatic progression from cross-sectional cancer genomics data | NetBio | Metastasis formation is a hallmark of cancer lethality. Yet, metastases are generally unobservable during their early stages_x000D_ of dissemination a [...] |
| 14 July 16:40-17:00 (add to calendar) | 518 | Noa Moriel | Optimal sequencing budget allocation for trajectory reconstruction of single cells | RegSys | Charting cellular trajectories over gene expression is key to understanding dynamic cellular processes and their underlying mechanisms. While advances [...] |
| 14 July 16:40-17:00 (add to calendar) | 524ab | Minbyul Jeong | Improving Medical Reasoning through Retrieval and Self-Reflection with Retrieval-Augmented Large Language Models | Text Mining | Recent proprietary large language models (LLMs), such as GPT-4, have achieved a milestone in tackling diverse challenges in the biomedical domain, ran [...] |
| 14 July 16:40-16:50 (add to calendar) | 524c | Philippe Youkharibache | Envisioning the OSE for Biology Research and Education | Visualizing Protein Function from Genes to Biology: Back to the Future | The project named iCn3D POSE (Pathway to an Open Source Ecosystem) holds the potential to drive transformative advancements in education and in resear [...] |
| 14 July 16:40-17:20 (add to calendar) | 519 | Jérôme Waldispühl | Fast and accurate RNA virtual screening using non-canonical RNA base pair interaction networks and graph machine learning | iRNA | RNAs constitute a vast reservoir of mostly untapped drug targets. Structure-based virtual screening (VS) methods are key to massively screen molecular [...] |
| 14 July 16:50-17:00 (add to calendar) | 524c | Community Hackathons | Visualizing Protein Function from Genes to Biology: Back to the Future | ||
| 14 July 17:00-18:00 (add to calendar) | 521 | Fritz Lekschas | The Insight’s in the Details: Challenges and Opportunities in Visually Exploring High-Dimensional BioMedical Data | BioVis | |
| 14 July 17:00-18:00 (add to calendar) | 521 | Award Ceremony and Closing | BioVis | ||
| 14 July 17:00-17:20 (add to calendar) | 520b | Giulia Babbi | Analysing multifunctional proteins with MultifacetedProtDB | Function | We recently proposed MultifacetedProtDB (https://multifacetedprotdb.biocomp.unibo.it), a curated database providing a collection of 1103 multifunction [...] |
| 14 July 17:00-17:20 (add to calendar) | 517d | Jonathan Bard | Maximizing accuracy of cellular deconvolution. (ACeD) | HiTSeq | Bulk RNA-sequencing has been a mainstay for biomedical research since its inception. In cancer alone, the TCGA project has examined 33 cancer types w [...] |
| 14 July 17:00-17:20 (add to calendar) | 520c | Multi-omics systems biology approach identifies novel signature genes for neuropsychiatric disorders | NetBio | The complex nature of mental disorders has long fascinated scientists, driving them to uncover the shared genetic factors that link these conditions. [...] | |
| 14 July 17:00-17:20 (add to calendar) | 518 | Ayan Paul | Charting the role of RNA binding proteins in tissue-specific alternative splicing using machine explanations | RegSys | The regulation of alternative splicing by RNA Binding Proteins (RBP) is an essential mechanism in determining tissue specificity. The nuances of the v [...] |
| 14 July 17:00-18:00 (add to calendar) | 524ab | Leveraging AI, text mining and large language models to advance biology and medicine | Text Mining | ||
| 14 July 17:00-18:00 (add to calendar) | 524c | Round Table Discussion | Visualizing Protein Function from Genes to Biology: Back to the Future | ||
| 14 July 17:05-17:30 (add to calendar) | 522 | Ulrike Steindl | Knowledge graphs in Cancer Genomics: The Case of Mutational Signatures | Bio-Ontologies | Mutational Signatures are generated from somatic genomic mutation data based on their sequence context and have been shown to be indicative of various [...] |
| 14 July 17:10-18:00 (add to calendar) | 525 | Breakout Groups | BioInfo-Core | Attendees will form breakout groups to discuss topics of interest from the day and other topics suggested by attendees in order to share knowledge and [...] | |
| 14 July 17:20-17:40 (add to calendar) | 520a | Fei Wang | FraGNNet: A Deep Probabilistic Model for Mass Spectrum Prediction | Bioinformatics in Canada | Tandem mass spectrometry (MS/MS) plays an important role in metabolomics analysis. MS/MS workflows attempt molecular structure inference from mass spe [...] |
| 14 July 17:20-17:40 (add to calendar) | 520b | Siyu Yang | Dynamic network analysis of multi-scale -omics data for protein function prediction | Function | Protein function prediction is a prominent computational task. One common approach is analyzing proteins' 3D structures by modeling them as protein st [...] |
| 14 July 17:20-17:40 (add to calendar) | 517d | Marjorie Roskes | Evolution of genomic and epigenomic heterogeneity in prostate cancer from tissue and liquid biopsy | HiTSeq | Castration Resistant Prostate Cancer (CRPC) is an aggressive disease that is highly plastic. Although histologically there are two subtypes of CRPC: a [...] |
| 14 July 17:20-17:40 (add to calendar) | 520c | Luis Augusto Eijy Nagai | Improved community detection through signed graphs in single-cell co-expression networks | NetBio | Recent advances in single-cell RNA sequencing (scRNA-seq) have highlighted the limitations of traditional gene co-expression network analysis in captu [...] |
| 14 July 17:20-18:00 (add to calendar) | 518 | Hae Kyung Im | Harnessing deep learning to amplify insights from GWAS | RegSys | Genome-wide Association Studies (GWAS) have identified associations with thousands of complex traits across a significant portion of the genome. Trans [...] |
| 14 July 17:20-17:40 (add to calendar) | 519 | Frederic Runge | Partial RNA Design | iRNA | RNA design is a key technique to achieve new functionality in fields like synthetic biology or biotechnology. Computational tools could help to find s [...] |
| 14 July 17:30-18:00 (add to calendar) | 522 | COSI Closing Remarks | Bio-Ontologies | Speaker Questions and COSI Closing / Community Discussion [...] | |
| 14 July 17:40-18:00 (add to calendar) | 520a | Jennifer Geddes-McAlister | Formation of the Canadian Artificial Intelligence and Mass Spectrometry Consortium (CAN-AIMS) | Bioinformatics in Canada | Disease spans diverse demographics and negatively impacts human health, affecting each individual in a specific manner. The ability to diagnose, monit [...] |
| 14 July 17:40-18:00 (add to calendar) | 520b | Jason Mcdermott | Enhanced Functional Annotation for Genome-Scale Metabolic Models Using an Omics-Informed Integrated Pipeline | Function | There are inherent challenges in characterizing the metabolic potential of complex microbiomes, particularly those derived from incomplete data like m [...] |
| 14 July 17:40-18:00 (add to calendar) | 517d | Rija Zaidi | Accurate and robust bootstrap inference of single-cell phylogenies by integrating sequencing read counts | HiTSeq | Recent single-cell DNA sequencing (scDNA-seq) technologies have enabled the parallel investigation of thousands of individual cells. This is required [...] |
| 14 July 17:40-18:00 (add to calendar) | 520c | Hao Zhu | Fast Gene Regulatory Network Inference in Single-cell RNA-Seq with RegDiffusion | NetBio | Understanding gene regulatory networks (GRNs) is crucial for elucidating cellular mechanisms and advancing therapeutic interventions. Many existing me [...] |
| 14 July 17:40-17:50 (add to calendar) | 519 | J. White Bear | High resolution deconvolution of RNA secondary structure via long read nanopore technology | iRNA | RNA are known to be highly flexible and take on multiple conformations to perform various tasks and binding in vivo. This makes structural analysis mo [...] |
| 14 July 17:50-18:00 (add to calendar) | 519 | Conclusion and awards | iRNA | ||
| 14 July 18:00-19:30 (add to calendar) | 524c | iCn3D Workshop | Visualizing Protein Function from Genes to Biology: Back to the Future | Target Audience: This workshop is designed for the 2024 International Conference on Intelligent Systems for Molecular Biology (ISMB). Tailored for bio [...] | |
| 15 July 09:00-10:00 (add to calendar) | 517d | Martin Steinegger | Supercharged Protein Analysis in the Era of Accurate Structure Prediction | Distinguished Keynotes | Abstract: Protein analysis has witnessed a revolution through machine-learning methods. At the forefront are highly accurate structure prediction meth [...] |
| 15 July 10:40-11:20 (add to calendar) | 520a | Janet M Thornton | 50 Years of Protein Structures & Structural Bioinformatics | 3DSIG | The last 50 years have seen a revolution in our understanding of proteins and how they work in 3D. This has been enabled by the development of many ne [...] |
| 15 July 10:40-11:00 (add to calendar) | 524ab | Opening Remarks | BOSC | ||
| 15 July 10:40-11:00 (add to calendar) | 524ab | Open Bioinformatics Foundation Update | BOSC | ||
| 15 July 10:40-11:00 (add to calendar) | 524ab | CoFest Intro | BOSC | ||
| 15 July 10:40-11:00 (add to calendar) | 524ab | Platinum and Gold Sponsor Videos | BOSC | ||
| 15 July 10:40-11:00 (add to calendar) | 520b | Welcome & Overview | CAMDA | ||
| 15 July 10:40-11:00 (add to calendar) | 522 | Aritra Bose | Epidemiological topology data analysis links severe COVID-19 to RAAS and hyperlipidemia associated metabolic syndrome conditions | Equity and Diversity in Computational Biology Research | The emergence of COVID-19 created incredible worldwide challenges but offers unique opportunities to understand the physiology of its risk factors and [...] |
| 15 July 10:40-11:00 (add to calendar) | 518 | Bertrand Marchand | Median and Small Parsimony Problems on RNA trees | EvolCompGen | Motivation:_x000D_ Non-coding RNAs (ncRNAs) express their functions by adopting molecular structures. Specifically, RNA secondary structures serve as [...] |
| 15 July 10:40-11:00 (add to calendar) | 519 | Xinrui Lyu | An Empirical Study on KDIGO-Defined Acute Kidney Injury Prediction in the Intensive Care Unit | General Computational Biology | Motivation: Acute kidney injury (AKI) is a syndrome that affects up to a third of all critically ill patients, and early diagnosis to receive adequate [...] |
| 15 July 10:40-11:30 (add to calendar) | 517d | How generative AI can transform biomedical research | MLCSB | This talk will explore how we can develop and use generative AI to help researchers. I will first discuss how generative AI can act as research co-adv [...] | |
| 15 July 10:40-11:20 (add to calendar) | 520c | Anne-Claude Gingras | Using proximity-dependent biotinylation to understand dynamic cell organization | NetBio | Compartmentalization is essential for all complex forms of life. In eukaryotic cells, membrane-bound organelles and a multitude of protein- and nuclei [...] |
| 15 July 10:40-11:00 (add to calendar) | 524c | Kedar Patwardhan | Utilizing Pre-Treatment Lab Values & Whole-Lung Radiomics for Modeling Survival Risk for ICB in the mNSCLC Setting | Tech Track | At AstraZeneca Oncology Data Science, we committed to unlock the potential of AI/ML-driven data science. Here we demonstrate that pre-treatment clinic [...] |
| 15 July 10:40-11:00 (add to calendar) | 521 | Opening Remarks | VarI | ||
| 15 July 10:40-11:00 (add to calendar) | 521 | Danielle Gutman | Exploring the landscape of regulatory uORFs in BMPR2 and their potential as therapeutic targets | VarI | About 50% of human genes harbor upstream open reading frames (uORFs), with a start codon in the 5’ untranslated region (5’UTR) occurring before the co [...] |
| 15 July 10:40-12:20 (add to calendar) | 525 | WEB 2024: Experiential Learning on How to Implement AI in Bioinformatics Training | WEB 2024: Experiential Learning on How to Implement AI in Bioinformatics Training | ||
| 15 July 11:00-11:20 (add to calendar) | 524ab | Paul Pavlidis | Gemma: Curation, re-analysis and dissemination of 18,000 gene expression studies | BOSC | Gemma (https://gemma.msl.ubc.ca) is an open source and open data project focused on increasing the utility of existing gene expression studies. While [...] |
| 15 July 11:00-12:20 (add to calendar) | 520b | Catherine Lozupone | CAMDA Keynote: Exploring drivers of gut microbiome compositional differences in disease and mechanistic pathways to recovery using big data | CAMDA | The commensal gut microbiome plays an essential role in protecting against opportunistic pathogens and maintaining immune homeostasis. Dysbiosis, an i [...] |
| 15 July 11:00-11:20 (add to calendar) | 522 | George Acquaah-Mensah | Disparate radiomic imaging features are predictive of recurrence events and molecular subtype in Black and White breast cancer patients | Equity and Diversity in Computational Biology Research | Breast cancer is among the deadliest cancers for women in the world. Breast cancer has four distinct molecular subtypes which are determined by gene e [...] |
| 15 July 11:00-11:20 (add to calendar) | 519 | Patrick Martin | Mapping spatial omics when tissue architecture doesn’t match. | General Computational Biology | The reality of using spatial transcriptomics in a clinical setting is that samples taken from different patients, under different conditions, and at d [...] |
| 15 July 11:00-11:20 (add to calendar) | 524c | Felipe Pérez-Jvostov | Enhancing Genomic Research through National Collaboration: The Role of Canada's National Data Platform | Tech Track | National data infrastructure is a critical enabler of Canada’s genomic research and community-driven collaboration. The success of such infrastructure [...] |
| 15 July 11:00-11:40 (add to calendar) | 521 | Jun Cheng | Beyond the sequence: interpreting missense variants with structure context | VarI | The vast majority of missense variants observed in the human genome are of unknown clinical significance. Machine learning approaches could close this [...] |
| 15 July 11:10-11:20 (add to calendar) | 518 | Wend Yam Donald Davy Ouedraogo | Inferring transcript phylogenies based on precomputed groups of conserved transcripts | EvolCompGen | Alternative Splicing (AS) is a mechanism in eukaryotic gene expression by which different combinations of introns are spliced to produce distinct tran [...] |
| 15 July 11:20-11:40 (add to calendar) | 520a | Samuel Sledzieski | Democratizing Protein Language Models with Parameter-Efficient Fine-Tuning | 3DSIG | Proteomics has been revolutionized by large protein language models (PLMs), which learn unsupervised representations from large corpora of sequences. [...] |
| 15 July 11:20-11:40 (add to calendar) | 524ab | Ida Shinder | EASTR: Identifying and eliminating systematic alignment errors in multi-exon genes | BOSC | Accurate RNA-seq alignment to reference genomes is fundamental to transcript assembly, annotation, and gene expression studies, integral to advancemen [...] |
| 15 July 11:20-11:40 (add to calendar) | 524ab | Jeffrey Roskes | ROC Picker: propagating statistical and systematic uncertainties in biological analyses | BOSC | We present the first version of ROC Picker, a software package for propagating statistical and systematic uncertainties in a biomedical analysis. The [...] |
| 15 July 11:20-11:40 (add to calendar) | 524ab | Iain Bancarz | Djerba: Sharing and Updating a Modular System for Clinical Report Generation | BOSC | Djerba is an open-source software package designed to streamline the translation of bioinformatic pipeline output from individual tumor samples into c [...] |
| 15 July 11:20-11:40 (add to calendar) | 524ab | Q&A For Flash Talks | BOSC | ||
| 15 July 11:20-11:40 (add to calendar) | 522 | Mona Singh | Towards Equitable MHC Binding Predictions: Computational Strategies to Assess and Reduce Data Bias | Equity and Diversity in Computational Biology Research | Deep learning tools that predict peptide binding by major histocompatibility complex (MHC) proteins play an essential role in developing personalized [...] |
| 15 July 11:20-11:40 (add to calendar) | 518 | Louxin Zhang | A Representation for Phylogenetic Trees and Networks | EvolCompGen | Good representations for phylogenetic trees and networks are important for human-computer interface and implementation of scalable heuristic methods f [...] |
| 15 July 11:20-11:40 (add to calendar) | 519 | Zoe Clarke | MALAT1 expression consistently indicates cell quality in single-cell RNA and single-nucleus RNA sequencing | General Computational Biology | Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq) have revolutionized our understanding of cell types, as it gives [...] |
| 15 July 11:20-11:40 (add to calendar) | 520c | Merel Kuijs | GraphCompass: Spatial metrics for differential analyses of cell organization across conditions | NetBio | Spatial omics technologies are increasingly leveraged to characterize how disease disrupts tissue organization and cellular niches. While multiple met [...] |
| 15 July 11:20-11:40 (add to calendar) | 524c | Alessia David | The Missense3D portal: Structure-based evaluation of missense variants including protein complexes and transmembrane regions | Tech Track | Missense3D (http://missense3d.bc.ic.ac.uk/) predicts the impact of missense variants on protein structure and reports their structural impact e.g. bur [...] |
| 15 July 11:30-11:40 (add to calendar) | 517d | Eric Sun | SPRITE: improving spatial gene expression imputation with gene and cell networks | MLCSB | Spatially resolved single-cell transcriptomics have provided unprecedented insights into gene expression {\it in situ}, particularly in the context of [...] |
| 15 July 11:40-12:00 (add to calendar) | 520a | Debswapna Bhattacharya | EquiPNAS: improved protein–nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks | 3DSIG | Protein language models (pLMs) trained on a large corpus of protein sequences have shown unprecedented scalability and broad generalizability in a wid [...] |
| 15 July 11:40-12:00 (add to calendar) | 524ab | Idowu Olawoye | Antimicrobial resistance prediction of nontuberculous mycobacteria from whole genome sequence data | BOSC | Nontuberculous mycobacteria (NTM) are opportunistic pathogens, predominantly causing pulmonary infections. NTMs are naturally resistant to many antibi [...] |
| 15 July 11:40-12:00 (add to calendar) | 522 | Selene L Fernandez-Valverde | From CABANA to CABANAnet – Building bioinformatics and knowledge exchange capacity in Latin America. | Equity and Diversity in Computational Biology Research | The CABANA project (Capacity Building for Bioinformatics in Latin America), funded by the UK's Global Challenges Research Fund from 2017 to 2022, aime [...] |
| 15 July 11:40-12:00 (add to calendar) | 518 | Anshu Gupta | Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES | EvolCompGen | Species tree inference is crucial in advancing our understanding of evolutionary relationships of life on Earth and has immense significance for diver [...] |
| 15 July 11:40-12:00 (add to calendar) | 519 | Kuan-Hao Chao | Combining DNA and protein alignments to improve genome annotation with LiftOn | General Computational Biology | As the number and variety of assembled genomes continues to grow, the number of annotated genomes is falling behind, particularly for eukaryotes. DNA- [...] |
| 15 July 11:40-12:00 (add to calendar) | 517d | Charles Broadbent | Deciphering High-order Structures in Spatial Transcriptomes with Graph-guided Tucker Decomposition | MLCSB | Spatial transcripome (ST) profiling can reveal cells’ structural organizations and functional roles in tissues. However, deciphering the spatial conte [...] |
| 15 July 11:40-12:00 (add to calendar) | 520c | Nadezhda T. Doncheva | Functional analysis of MS-based proteomics data: from protein groups to networks | NetBio | In high-throughput mass spectrometry (MS), proteins are digested into peptides and the peptide MS signals are then used to infer protein relative quan [...] |
| 15 July 11:40-12:00 (add to calendar) | 524c | Suzanne Paley | Integrated Pathway/Genome/Omics Informatics in Pathway Tools and BioCyc | Tech Track | An overview of the BioCyc website and Pathway Tools software suite, which features an extensive array of capabilities covering genome informatics, pat [...] |
| 15 July 11:40-12:00 (add to calendar) | 521 | Wim Vranken | Capturing biophysical and protein language model constraints for an improved assessment of the impact of mutations on protein function and stability | VarI | Our understanding of how proteins operate and how evolution shapes them is mainly based on their overall fold in relation to their amino acid sequence [...] |
| 15 July 12:00-12:20 (add to calendar) | 520a | Shuo Zhang | Accurate High-throughput Cryptic Binding Site Prediction Using Protein Language Model | 3DSIG | Identification of cryptic binding sites of proteins is an important but challenging task for understanding the function of proteins and screening pote [...] |
| 15 July 12:00-12:20 (add to calendar) | 524ab | Vedat Yilmaz | Open2C: Advancing 3D and functional genomics research | BOSC | Open2C (https://open2c.github.io) is a collaborative, open-source software community focused on advancing research in genome architecture and chromoso [...] |
| 15 July 12:00-12:20 (add to calendar) | 524ab | Stephanie Hao | A Framework for DNA Binding Motifs Prediction for Nontraditional Model Organism Transcription Factors | BOSC | To improve our predictions of phenotypic outcomes, it is essential to unravel the complex networks of genes and regulatory elements across different s [...] |
| 15 July 12:00-12:20 (add to calendar) | 524ab | Xi Zhang | Bioinformatics tools for comparative genomics analysis of highly similar duplicate genes in eukaryotic genomes | BOSC | Gene duplication plays an important role in evolutionary mechanism, which can act as a new source of genetic material in genome evolution. However, de [...] |
| 15 July 12:00-12:20 (add to calendar) | 524ab | Q&A For Flash Talks | BOSC | ||
| 15 July 12:00-12:20 (add to calendar) | 518 | Chun Wu | Generalized c/µ Ratio Test for Detecting Molecular Adaptation: Beyond the conventional Ka/Ks Ratio test without Assuming Synonymous Site Neutrality or Limitation to Translated Regions | EvolCompGen | The 60-year debate in evolutionary biology over "neutralist-selectionist" views demands a robust method to measure fitness changes due to mutations, y [...] |
| 15 July 12:00-12:20 (add to calendar) | 518 | Christophe Dessimoz | AlphaHOGs, a protein structure-based reference classification to improve orthology inference | EvolCompGen | The increasing availability of genomic sequences is driving forward our understanding of the diverse life forms on Earth. However, the ability to gene [...] |
| 15 July 12:00-12:20 (add to calendar) | 519 | Sanjana Tule | Optimal Phylogenetic Reconstruction of Insertion and Deletion Events. | General Computational Biology | Insertions and deletions (indels) influence the genetic code in fundamentally distinct ways from substitutions, significantly impacting gene product s [...] |
| 15 July 12:00-12:10 (add to calendar) | 517d | CellPie: a fast spatial transcriptomics factor discovery method via joint factorization of gene expression and imaging data | MLCSB | Spatially resolved transcriptomics has revolutionised the study of the gene expression within tissues, allowing researchers to maintain the spatial co [...] | |
| 15 July 12:00-12:20 (add to calendar) | 520c | Kevin Drew | Direct Contacts 2: identification of direct physical interactions from > 25,000 mass spectrometry experiments | NetBio | Protein complexes are essential to biological function and when disrupted can cause adverse health outcomes such as neurodegenerative disease, develop [...] |
| 15 July 12:00-12:20 (add to calendar) | 524c | Nicola Bordin | CATH and TED: Protein structure classification in the age of AI | Tech Track | CATH, now up-to-date with the Protein Data Bank, created with the group of David Jones at UCL the TED resource, classifying over 200m domains from AFD [...] |
| 15 July 12:00-12:20 (add to calendar) | 521 | Burkhard Rost | VespaG: Expert-guided protein Language Models enable accurate and blazingly fast fitness prediction | VarI | Exhaustively annotating the experimental effect of all known protein variants upon molecular protein function remains daunting and expensive. In respo [...] |
| 15 July 12:00-12:20 (add to calendar) | 521 | Oriol Gracia I Carmona | Addressing biases in large language models for variant impact prediction in macro proteins | VarI | Large multi-domain proteins pose significant challenges for both experimental studies and computational modelling due to their extensive size, often s [...] |
| 15 July 12:10-12:30 (add to calendar) | 517d | Sachin Mathur | Integrating patients in time series clinical transcriptomics data | MLCSB | Motivation: Analysis of time series transcriptomics data from clinical trials is challenging. Such studies usually profile very few time points from s [...] |
| 15 July 14:20-14:40 (add to calendar) | 520a | Rohit Singh | Contrastive learning in protein language space predicts interactions between drugs and protein targets | 3DSIG | Experimental screening of potential drug molecules against protein targets is a key bottleneck in the drug discovery pipeline. Fast and accurate compu [...] |
| 15 July 14:20-15:20 (add to calendar) | 524ab | Mélanie Courtot | The Data Shows We Need Better Data | BOSC | Big data, AI, LLMs… do they live up to the hype? In a bright and hopeful future, AI accelerates progress, revolutionizes healthcare, alerts us to heal [...] |
| 15 July 14:20-14:50 (add to calendar) | 520b | Kinga Zielińska | The Gut Microbiome based Health Index Challenge - Introduction | CAMDA | Microbiome-based disease prediction has significant potential as an early, non-invasive marker of multiple health conditions attributable to dysbiosis [...] |
| 15 July 14:20-14:40 (add to calendar) | 518 | Viola Chen | Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data | EvolCompGen | Eukaryotic cells contain organelles called mitochondria that have their own genome. Most cells contain thousands of mitochondria which replicate, even [...] |
| 15 July 14:20-14:40 (add to calendar) | 519 | Tanviben Patel | Approximating facial expression effects on diagnostic accuracy via generative AI | General Computational Biology | Artificial Intelligence (AI) is increasingly used in genomics research and practice, and generative AI has garnered significant recent attention. In c [...] |
| 15 July 14:20-15:10 (add to calendar) | 517d | Learning the Language of Biology: Transforming Biomedical Discovery with Foundation Models and Causal Inference | MLCSB | In this talk, I will showcase the work of my lab in revolutionizing biomedical data analysis through foundation models and large language models (LLMs [...] | |
| 15 July 14:20-14:40 (add to calendar) | 520c | Chao Deng | Identifying new cancer genes based on the integration of annotated gene sets via hypergraph neural networks | NetBio | Motivation: Identifying cancer genes remains a significant challenge in cancer genomics research. Annotated gene sets encode functional associations a [...] |
| 15 July 14:20-14:40 (add to calendar) | 524c | Paulina Dragan | GPCRVS – a machine learning system for GPCR drug discovery | Tech Track | GPCRVS (https://gpcrvs.chem.uw.edu.pl) is an efficient machine learning system for the online assessment of the compound activity against several GPCR [...] |
| 15 July 14:20-15:00 (add to calendar) | 521 | Heidi Rehm | Clinical classification of variation for disease causality | VarI | |
| 15 July 14:40-15:00 (add to calendar) | 520a | Thomas Descoteaux | NRGDock: An open-source software for ultra-massive high-throughput virtual screening | 3DSIG | Here we present NRGDock, an easy-to-use docking software based on Python requiring less than 0.5 CPU second per molecule. With this speed, a modern la [...] |
| 15 July 14:40-15:00 (add to calendar) | 519 | Mauminah Raina | Using Relation Equivariant Graph Neural Networks to Explore the Mosaic-like Tissue Architecture of Kidney Diseases with Spatially Resolved Transcriptomics | General Computational Biology | Chronic kidney disease is one of the leading public health problems with a prevalence of around 15% adults in the world. Emerging spatially resolved t [...] |
| 15 July 14:40-15:00 (add to calendar) | 520c | Mehmet Koyutürk | Are under-studied proteins under-represented? How to fairly evaluate link prediction algorithms in network biology | NetBio | For biomedical applications, new link prediction algorithms are continuously being developed and these algorithms are typically evaluated computationa [...] |
| 15 July 14:40-15:00 (add to calendar) | 524c | Modelling multi-omic, real-world data reveals immunogenomic drivers of resistance to cancer immunotherapy | Tech Track | At AstraZeneca’s Oncology Data Science, we committed to unlock the potential of AI/ML-driven data science. Here, we model clinical endpoints together [...] | |
| 15 July 14:50-15:20 (add to calendar) | 520b | Nelly Selem Mojica | Integrating Taxonomic and Functional Features for Gut Microbiome Health Indexing | CAMDA | This study aimed to enhance our understanding of metagenomic datasets by applying and innovating bioinformatics tools for the identification and funct [...] |
| 15 July 14:50-15:00 (add to calendar) | 518 | Jonghyun Lee | Tracking tumorigenesis and the transition state through copy number variation-based pseudotime | EvolCompGen | Driver mutations for different cancer types are extensively categorized. However, there appears to be no fixed number of driver mutations that guarant [...] |
| 15 July 15:00-15:20 (add to calendar) | 520a | Zuolong Zhang | Enhancing Generalizability and Performance in Drug-Target Interaction Identification by Integrating Pharmacophore and Pre-trained Models | 3DSIG | In drug discovery, it is crucial to assess the drug-target binding affinity. Although molecular docking is widely used, computational efficiency limit [...] |
| 15 July 15:00-15:20 (add to calendar) | 518 | Abigail Bunkum | SPICE: Probabilistic reconstruction of copy-number evolution in cancer | EvolCompGen | Somatic copy number alterations (SCNAs) are frequent genetic alterations that accumulate in tumour cells during cancer evolution and amplify or delete [...] |
| 15 July 15:00-15:20 (add to calendar) | 519 | Young Je Lee | scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics | General Computational Biology | Many popular spatial transcriptomics techniques lack single-cell resolution. Instead, these methods measure the collective gene expression for each lo [...] |
| 15 July 15:00-15:20 (add to calendar) | 520c | Joseph Szymborski | Protein Large Language Models are Effective, Generalized Protein-Protein Interaction Predictors | NetBio | Advancements in large language model (LLM) training have led to their widespread use across various applications, including predicting protein seconda [...] |
| 15 July 15:00-15:20 (add to calendar) | 524c | Decoding the grammar of DNA using Natural Language Processing | Tech Track | DNA is the blueprint defining all living organisms. Therefore, understanding the nature and_x000D_ function of DNA is at the core of all biological st [...] | |
| 15 July 15:00-15:20 (add to calendar) | 521 | Robert Kueffner | Ensemble Prediction of the Clinical Impact of Missense Variants Substantially Decreases VUS Rate in Genetic Testing | VarI | |
| 15 July 15:00-15:20 (add to calendar) | 521 | Dina Issakova | MAJIQ-CLIN: A novel tool for the identification of Mendelian disease-causing variants from RNA-seq data | VarI | Exome sequencing (ES) is the current standard of care for patients with suspected Mendelian genetic disorders. However, the diagnostic rate is only 25 [...] |
| 15 July 15:10-15:20 (add to calendar) | 517d | Jakub Zarzycki | Deep Reinforcement Learning for Controlled Traversing of the Attractor Landscape of Boolean Models in the Context of Cellular Reprogramming | MLCSB | Cellular reprogramming can be used for both the prevention and cure of different diseases. However, the efficiency of discovering reprogramming strate [...] |
| 15 July 15:20-15:40 (add to calendar) | 520a | Petras Kundrotas | DOCKGROUND: a new release of the long-standing resource for studying protein recognition | 3DSIG | Artificial intelligence (AI) has transformed the field of computational structural biology. Modeled structures of globular proteins now are accurate e [...] |
| 15 July 15:20-15:40 (add to calendar) | 524ab | Mitchell Shiell | Creating an open-source data platform. | BOSC | At BOSC 2023, we were excited to introduce Overture, a collection of open-source software used to overcome significant obstacles in storing, managing, [...] |
| 15 July 15:20-15:40 (add to calendar) | 520b | Patrick Smyth | Using Gradient Boosting to Predict Health States from Composition and Function of the Gut Microbiome | CAMDA | This study utilizes stool samples from the Human Microbiome Project 2 and American Gut Project cohorts, along with COVID-19 patient data, to develop a [...] |
| 15 July 15:20-15:40 (add to calendar) | 518 | Meaghan Parks | Uncovering Cancer's Fitness Landscape | EvolCompGen | CRISPR-based genome editing technologies have enabled massively-parallel genomic screens, such as DepMap – a Broad Consortium effort to catalog gene k [...] |
| 15 July 15:20-15:40 (add to calendar) | 519 | William Bowie | Multiview factorization for joint modeling of spatial multi-omics and histology images via NMF | General Computational Biology | An increasing number of cancer research studies employ spatially resolved transcriptomics (SRT) to investigate the composition of tumor microenvironme [...] |
| 15 July 15:20-15:40 (add to calendar) | 517d | Ding Bai | AttentionPert: Accurately Modeling Multiplexed Genetic Perturbations with Multi-scale Effects | MLCSB | Genetic perturbations (e.g. knockouts, variants) have laid the foundation for our understanding of many diseases, implicating pathogenic mechanisms an [...] |
| 15 July 15:20-15:40 (add to calendar) | 520c | Iker Núñez Carpintero | Addressing data scarcity in biomedical research using Multilayer Networks | NetBio | Realization of the new paradigm brought by Precision Medicine heavily relies on the development of integrative and cost-effective methodologies for an [...] |
| 15 July 15:20-15:40 (add to calendar) | 524c | Filippo Utro | Transform Healthcare and Life Sciencewith Biomedical Foundation modelsand Quantum computing | Tech Track | In the recent years, foundation models (FM) and quantum computing (QC) in healthcare and life science have sparked significant interests. This talk ex [...] |
| 15 July 15:20-15:40 (add to calendar) | 521 | Kivilcim Ozturk | Reclassifying variants of uncertain significance with transcriptional profiling | VarI | Understanding the functional impact of single amino acid substitutions in cancer driver genes remains an unmet need. Perturb-seq provides a tool to in [...] |
| 15 July 15:40-16:00 (add to calendar) | 520a | Marian Novotny | On finding the right match – a structural perspective | 3DSIG | Proteins can assume a number of 3D structural conformations during their lifetime and many of them can undergo a substantial conformational change tha [...] |
| 15 July 15:40-16:00 (add to calendar) | 524ab | Justin Richardsson | Going Viral: The Development of the VirusSeq Data Portal | BOSC | Tracking the evolution and spread of the COVID-19 virus prompted a rapid global initiative to sequence SARS-CoV-2 genomes. However, challenges arose c [...] |
| 15 July 15:40-16:00 (add to calendar) | 524ab | François Belleau | intermine.bio2rdf.org : A QLever SPARQL endpoint for InterMine databases | BOSC | This project explores converting biological data from InterMine, an open-source data warehouse, into a knowledge graph accessible via Bio2RDF. This ex [...] |
| 15 July 15:40-16:00 (add to calendar) | 524ab | Robert T. Giessmann | Organizing community curation to create an Open database on Thermodynamics of Enzyme-Catalyzed Reactions (openTECR) | BOSC | openTECR ("Open database on Thermodynamics of Enzyme-Catalyzed Reactions") is a database and a community. We create a data collection of apparent eq [...] |
| 15 July 15:40-16:00 (add to calendar) | 524ab | Q&A For Flash Talks | BOSC | ||
| 15 July 15:40-16:00 (add to calendar) | 520b | Karwowska Zuzanna | Microbiome time series data reveal predictable patterns of change | CAMDA | Despite the majority of microbiome studies being cross-sectional, it is widely acknowledged that the microbiome is a dynamic ecosystem. _x000D_ Here, [...] |
| 15 July 15:40-16:00 (add to calendar) | 518 | Valeriia Vasylieva | Measuring pseudogenes' kinship to unravel overlooked evolutionary patterns | EvolCompGen | Pseudogenes are defined as copies of protein-coding genes that have lost their ability to encode proteins and are functionless elements of our genomes [...] |
| 15 July 15:40-16:00 (add to calendar) | 518 | Dustin Hanke | Pseudogenes in plasmid genomes reveal past transitions in plasmid mobility | EvolCompGen | Evidence for gene non-functionalization due to mutational processes is found in genomes in the form of pseudogenes. Pseudogenes are known to be rare i [...] |
| 15 July 15:40-16:00 (add to calendar) | 519 | Erik Wright | Predicting gene functional associations from coevolutionary signals with EvoWeaver | General Computational Biology | The universe of uncharacterized proteins is expanding far faster than our ability to annotate their functions through laboratory study. Computational [...] |
| 15 July 15:40-16:00 (add to calendar) | 517d | Wei Huang | Predicting single-cell cellular responses to perturbations using cycle consistency learning | MLCSB | Phenotype-based screening has emerged as a powerful approach for identifying compounds that actively interact with cells. Transcriptional and proteom [...] |
| 15 July 15:40-16:00 (add to calendar) | 520c | Milan Picard | Target repositioning using multi-layer networks and machine learning: the case of prostate cancer | NetBio | The discovery of novel drug targets typically represents the first and most important step of drug discovery. One solution for target discovery is tar [...] |
| 15 July 15:40-16:00 (add to calendar) | 521 | Thomas Renne | Metacell burden: A method to quantify the effects on neurodevelopmental disorders of rare genomic variants aggregated across brain cells. | VarI | Neurodevelopmental disorders (NDs), such as autism or intellectual disabilities, affect up to 5% of the population. While the high heritability rate o [...] |
| 15 July 16:40-17:00 (add to calendar) | 520a | Valentin Lombard | Explaining Conformational Diversity in Protein Families through Molecular Motion | 3DSIG | Proteins play a central role in biological processes, and understanding their conformational variability is crucial for unraveling their functional me [...] |
| 15 July 16:40-17:00 (add to calendar) | 520a | Myungjin Lee | Pathway of transition for HIV-1 envelope trimer from prefusion-closed to CD4-bound open through an occluded-intermediate state | 3DSIG | HIV entry into host cells is initiated by the engagement of the gp120 subunit of the HIV-1 envelope (Env) trimer with the cellular receptor CD4. This [...] |
| 15 July 16:40-17:00 (add to calendar) | 524ab | Ann Loraine | Connecting Integrated Genome Browser to a huge genome database using its open API solves one problem and creates another | BOSC | Integrated Genome Browser (IGB, pronounced “ig-bee”) is a fast, feature-rich, open-source desktop genome browser thousands of researchers have used to [...] |
| 15 July 16:40-17:10 (add to calendar) | 520b | Jesse Shapiro | Prediction in microbiome science | CAMDA | As variation in microbial community structure is implicated in an increasing number of human diseases and environmental changes, there is strong poten [...] |
| 15 July 16:40-17:00 (add to calendar) | 518 | Yuri Wolf | Long range segmentation of prokaryotic genomes by gene age and functionality | EvolCompGen | Bacterial and archaeal genomes encompass numerous operons that typically consist of two to five genes. On larger scales, however, gene order is poorly [...] |
| 15 July 16:40-17:00 (add to calendar) | 519 | Domagoj Doresic | Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data | General Computational Biology | Quantitative dynamical models facilitate the understanding of biological processes and the prediction of their dynamics. The parameters of these model [...] |
| 15 July 16:40-17:00 (add to calendar) | 517d | Asa Ben-Hur | The role of chromatin state in intron retention: a case study in leveraging large scale deep learning models | MLCSB | Complex deep learning models trained on very large datasets have become key enabling tools for current research in natural language processing and co [...] |
| 15 July 16:40-17:00 (add to calendar) | 517d | Anupama Jha | Predicting interchromosomal Hi-C contacts from DNA sequence with TwinC | MLCSB | The 3D nuclear DNA architecture is composed of intrachromosomal and interchromosomal contacts. Despite the functional relevance of interchromosomal co [...] |
| 15 July 16:40-17:00 (add to calendar) | 520c | Dongmin Bang | Transfer Learning of Condition-Specific Perturbation in Gene Interactions Improves Drug Response Prediction | NetBio | Drug response is conventionally measured at the cell level, often quantified by metrics like IC50. However, to gain a deeper understanding of drug res [...] |
| 15 July 16:40-17:00 (add to calendar) | 519 | Introduction | TransMed | ||
| 15 July 16:40-17:00 (add to calendar) | 519 | Ian Overton | Quality Assurance, Semantic Enrichment and Integration of Multimodal Health Data for Phenotype and Cohort Discovery with Deep Learning | TransMed | Integration of data from multiple domains can greatly enhance the quality and applicability of knowledge generated in analysis workflows. However, wor [...] |
| 15 July 16:40-17:00 (add to calendar) | 521 | Patrick Wall | Representing Mutations for Predicting Cancer Drug Response | VarI | Motivation. Predicting cancer drug response requires a comprehensive assessment of many mutations present across a tumor genome. While current drug re [...] |
| 15 July 17:00-17:20 (add to calendar) | 520a | Aleksey Porollo | Analysis and prediction of RuBisCO kinetics using deep learning | 3DSIG | This study focuses on enhancing the efficiency of Calvin cycle by targeting the kinetic parameters of its key enzyme, Ribulose-1,5-bisphosphate carbox [...] |
| 15 July 17:00-17:20 (add to calendar) | 524ab | Carolyn T. Caron | Collaborating our way to optimal integration between Tripal 4 and JBrowse 2 | BOSC | To meet the diverse needs of their research communities, biological web portals not only strive to make data and their associated metadata accessible [...] |
| 15 July 17:00-17:20 (add to calendar) | 524ab | Colin Diesh | An integrated environment for browsing 3-D protein structures and multiple sequence alignments in JBrowse 2 | BOSC | Recent advances in protein structure prediction have invigorated research in protein structural biology. To enable the visualization of genomic datase [...] |
| 15 July 17:00-17:20 (add to calendar) | 524ab | Jiyao Wang | iCn3D, a Platform to Integrate Structures with Functions and Genomics | BOSC | With the improvement of structural prediction such as AlphaFold, a challenge is to integrate structures with functions and genomics. We started iCn3D [...] |
| 15 July 17:00-17:20 (add to calendar) | 524ab | Q&A For Flash Talks | BOSC | ||
| 15 July 17:00-17:20 (add to calendar) | 518 | Yiqing Wang | The evolution of antibiotic resistance islands occurs within the framework of plasmid lineages | EvolCompGen | Bacterial pathogens carrying multidrug resistance (MDR) plasmids are a major threat to human health. The acquisition of antibiotic resistance genes (A [...] |
| 15 July 17:00-17:20 (add to calendar) | 518 | Adena Collens | Elucidating the Co-Evolution and Genetic Diversity of Acquired Phototrophy in Marine Worm Convolutriloba longifissura | EvolCompGen | While instances of acquired phototrophy can be found across the eukaryotic tree of life, much about the evolution and maintenance of these endosymbiot [...] |
| 15 July 17:00-17:20 (add to calendar) | 519 | Emily Clough | NCBI’s RNA-seq analysis pipeline produces millions of pre-computed gene expression counts to accelerate data reuse and discovery | General Computational Biology | The NIH Sequence Read Archive (SRA) is a diverse collection of DNA and RNA sequences that together document the genetic diversity across the tree of l [...] |
| 15 July 17:00-17:20 (add to calendar) | 517d | Mogan Gim | MolPLA: A Molecular Pre-training Framework for Learning Cores, R-Groups and their Linker Joints | MLCSB | Motivation: Molecular core structures and R-groups are essential concepts especially in compound analysis and lead optimization. Integration of these [...] |
| 15 July 17:00-17:20 (add to calendar) | 520c | Rachel Melamed | Draphnet: Learning the drug and phenotype network linking drug effects to disease genetics | NetBio | Medications can have unexpected effects on disease, including not only harmful drug side effects, but also beneficial drug repurposing. These effects [...] |
| 15 July 17:00-17:20 (add to calendar) | 522 | Serdar Bozdag | TA-RNN: an Attention-based Time-aware Recurrent Neural Network Architecture for Electronic Health Records | TransMed | Motivation: Electronic Health Records (EHR) represent a comprehensive resource of a patient's medical history. EHR are essential for utilizing advance [...] |
| 15 July 17:00-17:20 (add to calendar) | 521 | Marina Abakarova | Assessing lethal missense mutations and polymorphism in Drosophila melanogaster with an evolutionary-informed model | VarI | This study investigates the impact of missense mutations on the Drosophila melanogaster proteome and contributes to our understanding of the genotype- [...] |
| 15 July 17:00-17:20 (add to calendar) | 521 | Thibault Latrille | A phylogenetic mutation-selection model predicts fitness effects of mutations in extant mammals | VarI | At the phylogenetic scale, sequence variation informs us on the selective effects of mutations. Indeed, mutations can be either beneficial, deleteriou [...] |
| 15 July 17:10-17:30 (add to calendar) | 520b | The Elephant in the Room: Software and Hardware Security Vulnerabilities of Portable Sequencing Devices | CAMDA | Portable genome sequencing technology is revolutionizing genomic research by providing a faster, flexible method of sequencing DNA and RNA. The unprec [...] | |
| 15 July 17:10-17:30 (add to calendar) | 520b | Improving genomic epidemiology of Giardia intestinalis with a core genome gene-by-gene subtyping schema | CAMDA | Giardia intestinalis parasites are common causes of sporadic gastroenteritis outbreaks in high-income countries. In contrast, giardiasis is endemic in [...] | |
| 15 July 17:20-17:40 (add to calendar) | 520a | Gabriel Galdino | Understanding and predicting ligand efficacy in the mu-opioid receptor through quantitative dynamical analysis of complex structures | 3DSIG | GPCRs are a family of membrane proteins that regulate many biological processes and are attractive targets for drug development, representing approxim [...] |
| 15 July 17:20-17:40 (add to calendar) | 524ab | Bhavesh Patel | Codefair: Make Biomedical Research Software FAIR Without Breaking a Sweat | BOSC | We present codefair, an innovative solution that helps researchers make their biomedical research software Findable, Accessible, Interoperable, and Re [...] |
| 15 July 17:20-17:40 (add to calendar) | 524ab | Hasindu Gamaarachchi | An Open-source Ecosystem For Scalable And Computationally Efficient Nanopore Data Processing | BOSC | Emerging long-read sequencing - recently dubbed “Nature Method of the Year” - has now become an important tool in understanding genomics. Nanopore is [...] |
| 15 July 17:20-17:40 (add to calendar) | 524ab | Avishai Weissberg | GenomeKit, a Python library for fast and easy access to genomic resources | BOSC | GenomeKit is Deep Genomics’ high performance Python library for fast and easy access to genomic resources such as sequence, data tracks, annotations, [...] |
| 15 July 17:20-17:40 (add to calendar) | 524ab | Q&A For Flash Talks | BOSC | ||
| 15 July 17:20-17:40 (add to calendar) | 518 | Yannis Nevers | Quality assessment of gene repertoires with OMArk | EvolCompGen | The amount and diversity of new genomes getting sequenced across the world opens the doors for large-scale comparative genomics. Thus, reliably ensuri [...] |
| 15 July 17:20-17:40 (add to calendar) | 519 | Jingtao Wang | Enabling Affordable Single-Cell Data in Large Cohort Studies via Deep Generative Neural Networks and Active Learning | General Computational Biology | Single-cell sequencing is a crucial tool for dissecting the cellular intricacies of complex diseases. Its prohibitive cost, however, hampers its appli [...] |
| 15 July 17:20-17:40 (add to calendar) | 517d | Yoseph Barash | Deep generative models for RNA splicing predictions and design | MLCSB | Alternative splicing (AS) of pre-mRNA is a highly regulated process with significant splicing changes occurring across human tissues. The tissue-speci [...] |
| 15 July 17:20-17:40 (add to calendar) | 517d | Daniel Olson | NEAR: Neural Embeddings for Amino acid Relationships | MLCSB | The homology search tool HMMER is extremely sensitive and can identify homologous protein pairs even when there is very little %id between them. Searc [...] |
| 15 July 17:20-18:00 (add to calendar) | 520c | Patrick Aloy | Blending Biology, Chemistry and AI through network embeddings | NetBio | Biological data is accumulating at an unprecedented rate, escalating the role of data-driven methods in computational drug discovery. The urge to coup [...] |
| 15 July 17:20-17:40 (add to calendar) | 519 | Panagiotis Nikolaos Lalagkas | Share genetics between breast cancer and its predisposing diseases identifies candidate drugs for repurposing for breast cancer | TransMed | The success of drugs targeting disease genes is widely acknowledged. However, identifying causal genes for common complex diseases remains a non-trivi [...] |
| 15 July 17:20-17:40 (add to calendar) | 519 | Emily Hoskins | Prevalence and biological impact of clinically relevant gene fusions in head and neck cancer | TransMed | Objective: Head and neck cancer (HNC) is the seventh most common cancer worldwide, with a 5-year survival rate of ~50%. The only existing genomic biom [...] |
| 15 July 17:20-18:00 (add to calendar) | 521 | Functional variomics for decoding variant effects | VarI | ||
| 15 July 17:30-17:50 (add to calendar) | 520b | Analysis of Inverted Repeats in Viral Genomes at a Large Scale | CAMDA | An inverted repeat (IR) in DNA is a sequence of nucleotides that is followed by its complementary bases but in reverse order (e.g., CACGGAttgTCCGTG). [...] | |
| 15 July 17:30-17:50 (add to calendar) | 520b | Intgration of Spatial Transcriptomics into Multimodal Imaging of Skin Aging | CAMDA | Advancements in spatial transcriptomicshave advanced our understanding of cellular organization and function within skin and other tissues. However, e [...] | |
| 15 July 17:40-18:00 (add to calendar) | 520a | Aydin Wells | Dynamic network analysis of protein structural change | 3DSIG | A protein’s sequence folds into a 3D structure, which directs what other proteins it may interact with to carry out cellular function. Hence, analyses [...] |
| 15 July 17:40-18:00 (add to calendar) | 524ab | Masaki Fukui | Tataki: Enhancing the robustness of bioinformatics workflows with simple, tolerant file format detection | BOSC | The increase in data volume in bioinformatics has heightened the demand for robust and reliable workflow analysis. Workflows enable the integration of [...] |
| 15 July 17:40-18:00 (add to calendar) | 524ab | Peter Amstutz | Arvados Project Update | BOSC | Arvados is a comprehensive, mature, open source platform for managing and processing large scale biomedical data on HPC and cloud. By combining robust [...] |
| 15 July 17:40-18:00 (add to calendar) | 524ab | Jayaram Kancherla | BiocPy: Facilitate Bioconductor Workflows in Python | BOSC | Bioconductor is an open-source software community that provides a rich repository of tools for the analysis and comprehension of genomic data. One of [...] |
| 15 July 17:40-18:00 (add to calendar) | 524ab | Q&A For Flash Talks | BOSC | ||
| 15 July 17:40-18:00 (add to calendar) | 518 | Ethan Wolfe | Leveraging machine learning to predict antimicrobial resistance in ESKAPE pathogens | EvolCompGen | Since the clinical introduction of antibiotics in the 1940s, antimicrobial resistance (AMR) has become an increasingly dire threat to global public he [...] |
| 15 July 17:40-18:00 (add to calendar) | 518 | Evan Brenner | Predicting pathogen preferences and host adaptation by leveraging microbial genomics and machine learning | EvolCompGen | Most emerging infectious diseases (EIDs) of humans originate in animals and are transmitted through zoonotic spillover events. However, the genetic de [...] |
| 15 July 17:40-18:00 (add to calendar) | 519 | Yashu Vashishath | HINN: A Novel Neural Network Architecture to Integrate Multi-Omics Data based on their Biological Relationships | General Computational Biology | Introduction: _x000D_ _x000D_ Methods: _x000D_ _x000D_ Results: _x000D_ _x000D_ Conclusion: [...] |
| 15 July 17:40-18:00 (add to calendar) | 517d | Jiri Reinis | Machine learning-enabled highly multiplexed monitoring of subcellular protein localization in live cells | MLCSB | Imaging-based methods are widely used for studying the subcellular localization of proteins in living cells. While routine for individual proteins, gl [...] |
| 15 July 17:40-18:00 (add to calendar) | 517d | Zhangzhi Peng | PTM-Mamba: A PTM-Aware Protein Language Model with Bidirectional Gated Mamba Blocks | MLCSB | Proteins serve as the workhorses of living organisms, orchestrating a wide array of vital functions. Post-translational modifications (PTMs) of their [...] |
| 15 July 17:40-18:00 (add to calendar) | 522 | Jian Liu | PhiHER2: Phenotype-informed weakly supervised model for HER2 status prediction from pathological images | TransMed | Motivation: HER2 status identification enables physicians to assess the prognosis risk and determine the treatment schedule for patients. In clinical [...] |
| 15 July 17:50-18:00 (add to calendar) | 520b | CAMDA 1st day summary | CAMDA | ||
| 16 July 08:30-08:50 (add to calendar) | 525 | Welcome and Introduction to SysMod! | SysMod | ||
| 16 July 08:40-09:20 (add to calendar) | 520a | Yana Bromberg | Metallic origins of life | 3DSIG | How did life appear on our planet? Alexander Oparin’s 1924 theory of abiotic evolution of carbon-based molecules in a primordial soup suggests a means [...] |
| 16 July 08:40-09:00 (add to calendar) | 524ab | Rayo Suseno | Enhancing Reproducibility in Immunogenetics: Leveraging Containerization Technology for Bioinformatics Workflows | BOSC | Bioinformatics is experiencing a crisis of reproducibility, which inhibits research progress and undermines scientific findings. This is driven by a v [...] |
| 16 July 08:40-10:00 (add to calendar) | 520b | Andrey Rzhetsky | Computational dissection of complex human disease | CAMDA | I will cover a collection of interrelated topics in dissection of etiology of complex human diseases, as seen through lens of large-scale medical data [...] |
| 16 July 08:40-08:41 (add to calendar) | 520c | Introductory remarks | Digital Agriculture | ||
| 16 July 08:40-09:00 (add to calendar) | 518 | Gary Hu | Maximum Likelihood Phylogeographic Inference of Cell Motility and Cell Division from Spatial Lineage Tracing Data | EvolCompGen | Recently developed spatial lineage tracing technologies induce somatic mutations at specific genomic loci in growing cells and then measure these muta [...] |
| 16 July 08:40-09:00 (add to calendar) | 517d | Natalie Davidson | Domain adaptation for cell-free DNA fragmentomics | MLCSB | Cell-free DNA (cfDNA) is an emerging minimally-invasive biomarker that could detect cancer, indicate transplant rejection, and predict autoimmune dise [...] |
| 16 July 08:40-09:00 (add to calendar) | 517d | Yang Lu | DeepROCK: Error-controlled interaction detection in deep neural networks | MLCSB | The complexity of deep neural networks (DNNs) makes them powerful but also makes them challenging to interpret, hindering their applicability in error [...] |
| 16 July 08:40-09:20 (add to calendar) | 519 | Heidi Rehm | Advancing Genomic Medicine through Clinical and Research Strategies | TransMed | Supporting genomics in research and medicine requires infrastructure, including standards, knowledgebases and global data sharing, as well as a rich i [...] |
| 16 July 08:41-09:20 (add to calendar) | 520c | Etienne Lord | Current and new development in Digital Agriculture – Implication of deep learning and robotics in this new data science | Digital Agriculture | Substainable agriculture faces many challenges since it must reconcile both agricultural productivity, while maintaining social, environmental and eco [...] |
| 16 July 08:50-09:30 (add to calendar) | 525 | Nathan Price | Keynote Speaker Talk: Digital twins and longitudinal deep phenotyping for preventive medicine and precision health | SysMod | Healthcare must become increasingly focused on extending healthspan and not only on treating disease after symptoms arise. Indeed, this transition is [...] |
| 16 July 09:00-09:20 (add to calendar) | 524ab | Nezar Abdennur | Breaking the silo: composable bioinformatics through cross-disciplinary open standards | BOSC | The practice of data science in genomics and computational biology is fraught with friction. This is largely due to a tight coupling of bioinformatic [...] |
| 16 July 09:00-09:20 (add to calendar) | 522 | Gregoire Altan-Bonnet | Building models of CAR-T signal integration, _x000B_using automatized/dynamic high-dimensional dynamic profiling | Computational and Systems Immunology | We present an experimental/theoretical pipeline to build quantitative models of leukocyte activation. We introduce a robotic platform to quantify the [...] |
| 16 July 09:00-09:20 (add to calendar) | 517d | Stefan Schrod | CODEX: COunterfactual Deep learning for the in-silico EXploration of cancer cell line perturbations | MLCSB | Motivation: High-throughput screens (HTS) provide a powerful tool to decipher the causal effects of chemical and genetic perturbations on cancer cell [...] |
| 16 July 09:10-09:20 (add to calendar) | 518 | Hoi Man Chung | Interpretable variational encoding of genotypes identifies comprehensive clonality and lineages in single cells geometrically | EvolCompGen | Despite the wide accessibility of genetic information in multiple omics assays, analyzing single-cell _x000D_ genomics remains a challenge due to its [...] |
| 16 July 09:20-09:40 (add to calendar) | 520a | Jianlin Cheng | De Novo Atomic Protein Structure Modeling for Cryo-EM Density Maps Using 3D Transformer and Hidden Markov Model | 3DSIG | Accurately building three-dimensional (3D) atomic structures from 3D cryo-electron microscopy (cryo-EM) density maps is a crucial step in the cryo-EM- [...] |
| 16 July 09:20-09:40 (add to calendar) | 524ab | Luis Pedro Coelho | For long-term sustainable software in bioinformatics: a manifesto | BOSC | I will discuss the challenges of maintaining research software in bioinformatics, especially considering the transient nature of funding and the turno [...] |
| 16 July 09:20-09:40 (add to calendar) | 524ab | Jonathon Keeney | BioCompute: A Descriptive Standard for Computable Metadata | BOSC | Scientific review of work in the life sciences has been hindered by a lack of standards relating to the communication of computational pipelines. Ofte [...] |
| 16 July 09:20-09:40 (add to calendar) | 524ab | Alberto Pepe | Breaking Down Research Silos and Fostering Radical Collaboration through Collective Intelligence | BOSC | The data landscape is rapidly expanding. Scientists are required to navigate increasing amounts of multimodal data in an attempt to create high-qualit [...] |
| 16 July 09:20-09:40 (add to calendar) | 524ab | Q&A For Flash Talks | BOSC | ||
| 16 July 09:20-09:40 (add to calendar) | 522 | TBD | Computational and Systems Immunology | ||
| 16 July 09:20-09:40 (add to calendar) | 520c | Steven Maere | Single-plant omics : profiling individual plants in a field to identify processes affecting yield | Digital Agriculture | Historically, processes influencing plant phenotypes have been studied intensively under controlled laboratory conditions. However, the results of suc [...] |
| 16 July 09:20-09:40 (add to calendar) | 518 | Juliette Luiselli | Genome streamlining: effect of mutation rate and population size on genome size reduction | EvolCompGen | Genome size reduction, also known as genome streamlining, is observed in bacteria with very different life traits, including endosymbiotic bacteria an [...] |
| 16 July 09:20-09:40 (add to calendar) | 518 | Felix Langschied | Evolutionary dynamics of microRNAs pinpoint innovations in the gene regulatory network of vertebrates | EvolCompGen | The evolution of the regulatory network formed by miRNAs and their target mRNAs remains poorly understood because scalable and accurate frameworks for [...] |
| 16 July 09:20-09:40 (add to calendar) | 517d | Divya Koyyalagunta | A statistical method for migration history inference reveals alternative patterns of metastatic dissemination, clonality and phyleticity | MLCSB | Although metastasis is the cause of 90% of cancer deaths, little is known about its clonal evolution, genetic drivers, and seeding patterns. Identifyi [...] |
| 16 July 09:20-09:40 (add to calendar) | 517d | Sungjoon Park | A deep learning model of tumor cell architecture elucidates response and resistance to CDK4/6 inhibitors | MLCSB | Cyclin-dependent kinase 4 and 6 inhibitors (CDK4/6is) have revolutionized breast cancer therapy. However, <50% of patients have an objective response, [...] |
| 16 July 09:20-09:40 (add to calendar) | 519 | Irene Mei | Transcriptional modulation unique to vulnerable motor neurons predict ALS across species and SOD1 gene mutations | TransMed | Amyotrophic lateral sclerosis (ALS) is characterized by the progressive loss of somatic motor_x000D_ neurons (MNs), which innervate skeletal muscles. [...] |
| 16 July 09:20-09:40 (add to calendar) | 519 | Javad Rahimikollu | Multi-dimensional Integration of PPI Network with Genetic and Molecular Data to Decipher the Genetic Underpinnings of RA Endotypes | TransMed | Rheumatoid arthritis (RA) is a complex autoimmune disease with polyetiological genetic basis. Serum rheumatoid factor (RF) and anti-citrullinated pept [...] |
| 16 July 09:30-09:50 (add to calendar) | 525 | Mingyang Lu | Building high quality dynamical models of gene regulatory circuits driving cellular state transitions using scRNA-seq data | SysMod | A major question in systems biology is to elucidate the gene regulatory mechanisms of cellular state transitions during developmental processes like c [...] |
| 16 July 09:40-10:00 (add to calendar) | 520a | Han Huang | RiboDiffusion: Tertiary Structure-based RNA Inverse Folding with Generative Diffusion Models | 3DSIG | RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fund [...] |
| 16 July 09:40-10:00 (add to calendar) | 524ab | Lacey-Anne Sanderson | Tripal: a community-driven framework supporting open science, sustainable data web portals | BOSC | As the open science movement gains momentum, UNESCO is highlighting the need for infrastructure to (1) support building of global, inclusive research [...] |
| 16 July 09:40-10:00 (add to calendar) | 522 | Kenneth Hoehn | Inferring B cell phylogenies from single cell and bulk BCR sequence data with Dowser | Computational and Systems Immunology | Antibodies are vital to human immune responses and are composed of genetically variable heavy and light chains. These structures are initially express [...] |
| 16 July 09:40-10:00 (add to calendar) | 520c | Hayda Almeida | Biomarker-based learning for disease prediction in precision dairy farming | Digital Agriculture | Metabolic diseases have great impact on dairy production and animal welfare [1, 2]. Metabolomic profiling has helped identify biomarkers to predict di [...] |
| 16 July 09:40-10:00 (add to calendar) | 518 | Priya | PHALCON: Phylogeny-aware variant calling from large-scale single-cell panel sequencing datasets | EvolCompGen | Single-cell sequencing (SCS) technologies bring cellular resolution in resolving intra-tumor heterogeneity, which can cause drug resistance and relaps [...] |
| 16 July 09:40-10:00 (add to calendar) | 517d | Monica-Andreea Baciu-Dragan | oncotree2vec – A method for embedding and clustering of tumor mutation trees | MLCSB | Understanding the genomic heterogeneity of tumors is an important task in computational oncology, especially in the context of finding personalized tr [...] |
| 16 July 09:40-10:00 (add to calendar) | 519 | Juan Carvajal | AI Epilepsy: Software solution to aid in the diagnosis of epilepsy using machine learning algorithms | TransMed | Epilepsy is a chronic neurological disorder characterized by recurrent seizures, affecting approximately 50 million people worldwide. Different method [...] |
| 16 July 09:40-10:00 (add to calendar) | 519 | Utkarsh Rai | HTJ2K as a Default Storage Format for Medical Images | TransMed | Healthcare systems around the world store large volumes of medical images, like X-rays or scans. The largest public archive currently has 30.9 million [...] |
| 16 July 09:50-10:00 (add to calendar) | 525 | Humza Hemani | Deciphering epigenetic regulatory mechanisms of IFNg-induced Epithelial to Mesenchymal Transition in human breast cells using systems approach | SysMod | Epigenetics changes within the cellular microenvironment play a significant role in both normal tissue development and the initiation and advancement [...] |
| 16 July 10:40-10:50 (add to calendar) | 520a | Philippe Youkharibache | Positional Protein Bioinformatics: A universal residue numbering scheme for the Immunoglobulin (Ig) fold enables its systemic detection in the protein universe. | 3DSIG | The Immunoglobulin fold (Ig-fold) is the most populous fold in the human proteome, found in proteins from all domains of life, with current (under)est [...] |
| 16 July 10:40-11:40 (add to calendar) | 524ab | Andrew Su | Open Data, Knowledge Graphs, and Large Language Models | BOSC | Bioinformatics is the science of collecting, storing, analyzing, and disseminating biological data and information. As in most domains of data science [...] |
| 16 July 10:40-11:10 (add to calendar) | 520b | Joaquin Dopazo | The Synthetic Clinical Health Records Challenge - Introduction | CAMDA | Although data protection is necessary to preserve patients’ intimacy, privacy regulations are also an obstacle to biomedical research. An interesting [...] |
| 16 July 10:40-11:00 (add to calendar) | 522 | TBD | Computational and Systems Immunology | ||
| 16 July 10:40-10:40 (add to calendar) | 524c | Welcome & Introductions | Demystifying the World of Scientific Publishing | ||
| 16 July 10:40-11:00 (add to calendar) | 524c | Patricia Palagi | Publishing reproducibility, FAIR, and using best practices | Demystifying the World of Scientific Publishing | In this talk, I will introduce the role scientific journals play in research reproducibility and the adoption of Open and FAIR (Findable, Accessible, [...] |
| 16 July 10:40-11:00 (add to calendar) | 524c | Alex Bateman | Use of LLMs in writing, plagiarism and text recycling | Demystifying the World of Scientific Publishing | |
| 16 July 10:40-11:00 (add to calendar) | 520c | Vahid Naghashi | Empowering Dairy Farmers: A Transformer-Based Framework for Informed Decision Making in Dairy Agriculture | Digital Agriculture | In precision livestock, the decision of animal replacement requires an estimation of the lifetime profit of the animal based on multiple factors and o [...] |
| 16 July 10:40-11:00 (add to calendar) | 518 | Tal Pupko | A machine-learning based alternative to phylogenetic bootstrap | EvolCompGen | Currently used methods for estimating branch support in phylogenetic analyses often rely on the classic Felsenstein's bootstrap, parametric tests, or [...] |
| 16 July 10:40-11:30 (add to calendar) | 517d | Sara Mostafavi | Deep learning of personal genomes | MLCSB | |
| 16 July 10:40-11:00 (add to calendar) | 525 | Tatum Liparulo | Mathematical Modeling suggests that Monocyte Activity may drive Sex Disparities during Influenza Infection | SysMod | In humans, females of reproductive age are at greater risk than their male, age-matched counterparts for hospitalization and death from influenza infe [...] |
| 16 July 10:40-11:20 (add to calendar) | 519 | Quaid Morris | The challenges of clinical deployment of automated cancer type classification for routine use | TransMed | Accurate cancer type classifiers would have profound impact on the success of cancer treatment. Each year, in the US, more than 30,000 people present [...] |
| 16 July 10:50-11:10 (add to calendar) | 520a | Dongjun Guo | ImmunoMatch: Illuminating the design of antibody heavy and light chain pairs using deep learning approaches and structure analysis | 3DSIG | Antibodies are composed of heavy (H) and light (L) chains. Sequence variations of H and L chains therefore combinatorially contribute to a diverse ant [...] |
| 16 July 11:00-11:20 (add to calendar) | 522 | Alireza Karbalayghareh | Learning multiomic velocities of dynamic germinal center B cells using single-cell multiome | Computational and Systems Immunology | The epigenome and transcriptome influence each other in differentiation trajectories. We use single cell multiomic data, with RNA expression and chrom [...] |
| 16 July 11:00-11:20 (add to calendar) | 524c | David Landsman | Open Access Publishing: pros and cons | Demystifying the World of Scientific Publishing | Open access for publicly funded research manuscripts has been available for close to 30 years. Following this move, there have been significant change [...] |
| 16 July 11:00-11:20 (add to calendar) | 524c | Thomas Lengauer | Strategies for managing expectations for submission, review, and publication timeline | Demystifying the World of Scientific Publishing | |
| 16 July 11:00-11:20 (add to calendar) | 520c | Kuan Y. Chang | Anomaly Detection for Smart Aquaculture: Predicting Water Color Changes in Grouper Ponds | Digital Agriculture | Healthy grouper farms thrive on "green water," indicating a balanced ecosystem. A shift to brown water, however, signals potential problems. This stud [...] |
| 16 July 11:00-11:20 (add to calendar) | 525 | Jennifer Riccio | Predictive Modeling and Experimental Control of Macrophage Pro-Inflammatory Dynamics | SysMod | Macrophages are immune cells which play a key role in the reaction to biomaterials. They exhibit a functional phenotype (or state) induced by the stim [...] |
| 16 July 11:10-11:30 (add to calendar) | 520a | Miriam Poley-Gil | Exploring the biophysical boundaries of protein families with deep learning methods | 3DSIG | Recently, Deep Learning models have revolutionised the Molecular Biology field allowing us to explore the intricate interplay between protein sequence [...] |
| 16 July 11:10-11:30 (add to calendar) | 520b | Daniel Voskergian | Predicting Diabetes Complications from Electronic Health Record Visits Using Machine Learning Algorithms | CAMDA | This study employed a novel approach to feature engineering, utilizing XGB feature selection combined with various supervised machine learning algorit [...] |
| 16 July 11:10-11:20 (add to calendar) | 518 | Soham Dibyachintan | Neutral variation in a protein interaction network limits predictability of protein evolution | EvolCompGen | The evolutionary fate of a mutation is dependent on its phenotypic effects. In recent years, multiple evolutionary models have been developed that use [...] |
| 16 July 11:20-11:40 (add to calendar) | 522 | Jane Siwek | Sliding Window INteraction Grammar (SWING): a generalized interaction language model for peptide and protein interactions | Computational and Systems Immunology | Language models (LMs) and protein LMs have now been employed in many frameworks. Traditionally for protein-protein or peptide-protein interactions (PP [...] |
| 16 July 11:20-11:40 (add to calendar) | 524c | Scott Edmunds | Challenges with reviewers: reviewing fatigue, acknowledgement, and dealing with delays and rejections. | Demystifying the World of Scientific Publishing | This talk will provide some experience from two decades at the coalface of editing journals on how peer review works behind the scenes. And the challe [...] |
| 16 July 11:20-11:40 (add to calendar) | 524c | Jason Papin | Emerging Trends in Publishing Computational Biology Research | Demystifying the World of Scientific Publishing | I will discuss initiatives at PLOS Computational Biology to address challenges in reproducibility and open access. I will share the genesis of several [...] |
| 16 July 11:20-11:40 (add to calendar) | 520c | Thomas Gisiger | Extracting meaningful video segments using a movement detection algorithm applied to dairy cow behavior study and welfare monitoring. | Digital Agriculture | Precision dairy farming is essential to creating a food production system that is durable and respects animal welfare and the environment._x000D_ _x00 [...] |
| 16 July 11:20-11:40 (add to calendar) | 518 | Mathieu Gascon | Simultaneously Building and Reconciling a Synteny Tree | EvolCompGen | Our lab recently presented Synesth (for SYNteny Evolution in SegmenTal Histories), an extended reconciliation model for synteny trees accounting for f [...] |
| 16 July 11:20-11:40 (add to calendar) | 525 | Imran Shah | Deciphering Cellular Fate Decisions: A Boolean Network Approach to Stress Response Network Tipping Points | SysMod | Adaptive stress response networks (SRNs) are invoked when chemical exposures induce DNA damage, oxidative stress, unfolded proteins, hypoxia, or heat [...] |
| 16 July 11:20-11:40 (add to calendar) | 519 | Mariam Khanfar | CIViC - an open-access knowledgebase for community driven curation of clinical variants in cancer | TransMed | In the era of personalized oncology, identifying clinically relevant variants is critical due to the rapidly increasing variant data and need for cons [...] |
| 16 July 11:20-11:40 (add to calendar) | 519 | Sasha Blay | Timing the development of chemoresistance in relapsed pediatric cancer | TransMed | Survivors of pediatric cancer face lifelong battles with severe morbidities, including a significant risk of recurrence. Mutational signatures are pat [...] |
| 16 July 11:30-11:40 (add to calendar) | 520a | Michael Schroeder | Can proteins be represented through secondary structures? | 3DSIG | Recent advancements in protein classification, driven by Foldseek for tertiary structure-based searches, raise the question of whether a simplified se [...] |
| 16 July 11:30-11:50 (add to calendar) | 520b | Daniel Santana-Quinteros | Cluster-based machine learning prediction of diabetes complications | CAMDA | Background: Type 2 Diabetes Mellitus (T2D) is a prevalent metabolic disorder characterized by hyperglycemia due to defects in insulin secretion or act [...] |
| 16 July 11:30-11:40 (add to calendar) | 517d | Linh Tran | ConfuseNN: Interpreting convolutional neural network inferences in population genomics with data shuffling | MLCSB | Convolutional neural network (CNN) is an increasingly popular supervised machine learning approach that has been applied to many inference tasks in po [...] |
| 16 July 11:40-12:00 (add to calendar) | 520a | Thomas Litfin | SPfast: Highly efficient protein structure alignment with segment-level representations and block-sparse optimization | 3DSIG | Recent advances in protein structure modelling have increased the availability of high-quality protein structures at an unprecedented scale. Newly ava [...] |
| 16 July 11:40-12:00 (add to calendar) | 520a | Alexander Monzon | STRPsearch: fast detection of structured tandem repeat proteins | 3DSIG | State-of-the-art prediction methods are generating millions of publicly available protein structures. Structured Tandem Repeats Proteins (STRPs) const [...] |
| 16 July 11:40-12:00 (add to calendar) | 524ab | Marcin Joachimiak | Gene Set Summarization Using Large Language Models | BOSC | Molecular biologists often use statistical enrichment analysis to interpret gene lists derived from high-throughput experiments and computational anal [...] |
| 16 July 11:40-12:20 (add to calendar) | 522 | Michael Klausen | Improved Peptide-MHC Interaction Predictions through Deep Generative Adversarial Networks and a Unified MHC Class I and Class II Representation | Computational and Systems Immunology | In this study, we address the challenge of accurately predicting peptide presentation by Major Histocompatibility Complex (MHC) molecules, a key featu [...] |
| 16 July 11:40-12:20 (add to calendar) | 522 | Ha Young Kim | TSpred: a robust prediction framework for TCR-epitope interactions using paired chain TCR sequence data | Computational and Systems Immunology | Prediction of T-cell receptor (TCR)-epitope interactions is important for many applications in biomedical research, such as cancer immunotherapy and v [...] |
| 16 July 11:40-12:20 (add to calendar) | 522 | Susanna Kiwala | Comprehensive neoantigen identification and prioritization using pVACtools and pVACview | Computational and Systems Immunology | Personalized neoantigen vaccines utilize immunogenomics and immuno-oncology strategies to combat cancer. Somatic variants in tumor cells generate neoa [...] |
| 16 July 11:40-12:20 (add to calendar) | 522 | Ayshwarya Subramanian | Immune checkpoint molecule Tim-3 regulates microglial function and the development of Alzheimer’s disease pathology. | Computational and Systems Immunology | Microglia are the major resident innate immune cells of the central nervous system (CNS) playing essential roles in CNS homeostasis and disease. Altho [...] |
| 16 July 11:40-12:20 (add to calendar) | 522 | Sarah Walker | Single-cell multi-omics reveals similarity between progenitor stem-cell-like CD8+ T cells and CD4+ follicular helper T cells in viral infection | Computational and Systems Immunology | Mechanisms of gene expression regulation in T cell activation and differentiation across lineages and functional states are incompletely understood. T [...] |
| 16 July 11:40-12:20 (add to calendar) | 522 | Sara Capponi | Optimizing CAR T cell design using quantum convolutional neural networks | Computational and Systems Immunology | Chimeric antigen receptor (CAR) T-cells are promising new medicines that apply to the treatment of many cancers, and potentially represent novel appro [...] |
| 16 July 11:40-12:20 (add to calendar) | 522 | Seda Arat | A Computational Approach to Auto-Immunity Risk Assessment: Use Cases of Molecular Mimicry Hypothesis for Viral Infections and Vaccines-Associated Adverse Events | Computational and Systems Immunology | SARS-CoV-2 virus is a member of a large family of viruses called coronaviruses that causes a respiratory disease COVID-19. There are almost 775 millio [...] |
| 16 July 11:40-12:15 (add to calendar) | 524c | Panel Discussion | Demystifying the World of Scientific Publishing | ||
| 16 July 11:40-12:00 (add to calendar) | 520c | Amanda Ashley Boatswain Jacques | Precision Farming for Profit: Leveraging Profitability Maps and ILPMZ to Optimize Return on Investment and Soil Conservation of Agricultural Fields | Digital Agriculture | Implementing site-specific management practices like profitability zones aids in stabilizing long-term profits while conserving the environment. Profi [...] |
| 16 July 11:40-12:00 (add to calendar) | 518 | Inanc Birol | ntSynt: multi-genome synteny detection using minimizer graph mappings | EvolCompGen | In recent years, the landscape of reference-grade genome assemblies has seen substantial diversification. With such rich data, there is pressing deman [...] |
| 16 July 11:40-12:30 (add to calendar) | 517d | Trustworthy AI in the life sciences | MLCSB | ||
| 16 July 11:40-12:00 (add to calendar) | 525 | Matteo Barberis | Integrative Systems and Synthetic Biology identifies a Yeast Minimal Cell Cycle network that coordinates cell proliferation dynamics | SysMod | The eukaryotic cell cycle is driven by waves of cyclin-dependent kinase (cyclin/Cdk) activities that rise and fall with a timely pattern called “waves [...] |
| 16 July 11:40-12:00 (add to calendar) | 519 | Jiaqi Li | PHENO-DEX: Phenotypic Mapping of Dexamethasone Response in Breast Cancer Cells using Single-cell Transcriptomics | TransMed | Identifying tumor heterogeneity in response to treatment prior to clinical intervention is critical for long-term survival. We’ve developed an AI-base [...] |
| 16 July 11:40-12:00 (add to calendar) | 519 | Hatice Osmanbeyoglu | Spatial landscape of malignant pleural and peritoneal mesothelioma tumor immune microenvironment | TransMed | Immunotherapies have shown modest clinical benefit thus far for malignant mesothelioma (MM). A deeper understanding of immune cell spatial distributio [...] |
| 16 July 11:50-12:20 (add to calendar) | 520b | Owen Visser | Statistical Measures for the Evaluation of Clustering Methods on Single Cell Data | CAMDA | The growing efficiency of single-cell sequencing technology has provided biologists with ample cells to identify and differentiate, often through clus [...] |
| 16 July 12:00-12:20 (add to calendar) | 520a | Nicola Bordin | The Encyclopedia of Domains | 3DSIG | The Encyclopaedia of Domains (TED) is a comprehensive classification of all globular protein structure domains in AlphaFold Database v4. Harnessing st [...] |
| 16 July 12:00-12:20 (add to calendar) | 524ab | Hilmar Lapp | FAIR, modular and reproducible image-based ML workflows for biologists: a template and case study from imageomics | BOSC | Machine Learning (ML) has become a critical tool in the life sciences, and is being applied to diverse biological data types, including the rapidly gr [...] |
| 16 July 12:00-12:20 (add to calendar) | 520c | Voncarlos Marcelo De Araujo | Revolutionizing Livestock Monitoring: AI-Powered Cow Detection in Farm Environments | Digital Agriculture | In modern agricultural management, ensuring accurate estimations of livestock population density within farm environments is essential. Our focus lies [...] |
| 16 July 12:00-12:20 (add to calendar) | 525 | Vishvak Raghavan | Harnessing Agent-Based Modeling in CellAgentChat to Unravel Cell-Cell Interactions from Single-Cell Data | SysMod | Understanding cell-cell interactions (CCIs) is essential yet challenging due to the inherent intricacy and diversity of cellular dynamics. Existing ap [...] |
| 16 July 12:00-12:20 (add to calendar) | 519 | Poster Flash Talks | TransMed | ||
| 16 July 12:15-12:20 (add to calendar) | 524c | Closing | Demystifying the World of Scientific Publishing | ||
| 16 July 14:20-14:40 (add to calendar) | 524ab | Chris Armit | Trust and Transparency in Reporting Machine Learning: The DOME-GigaScience Press Trial | BOSC | Machine learning is increasingly applied to biological and biomedical data, and there is a need for sufficient detail to enable a researcher to unders [...] |
| 16 July 14:20-14:25 (add to calendar) | 520b | The Anti-Microbial Resistance Prediction Challenge - Introduction | CAMDA | ||
| 16 July 14:20-14:40 (add to calendar) | 522 | TBD | Computational and Systems Immunology | ||
| 16 July 14:20-14:40 (add to calendar) | 520c | Houda Orchi | Temporal Synchronization of Multi-View Video for Cattle Movement Analysis in Dynamic Farm Settings | Digital Agriculture | Synchronizing and aligning multi-angle video footage is an intricate task in computer vision, especially in complex environments like barn settings, w [...] |
| 16 July 14:20-14:40 (add to calendar) | 518 | Maureen Stolzer | Automated clade-level detection of Incomplete lineage sorting | EvolCompGen | Phylogenetic population modeling, combined with sequencing of large collections of closely related taxa, has enabled unprecedented exploration of popu [...] |
| 16 July 14:20-15:10 (add to calendar) | 517d | Mor Nitzan | Towards spatiotemporal design principles in multicellular systems | MLCSB | Gene expression profiles of a cellular population, generated by single-cell RNA sequencing, contain rich, 'hidden' information about biological state [...] |
| 16 July 14:20-14:40 (add to calendar) | 525 | Da-Wei Lin | Metabolic Objectives and Trade-offs in Single-cells during Cellular Transitions | SysMod | Cell-type transitions, crucial for processes including cell quiescence, cell cycle, and embryogenesis, involve intricate metabolic rewiring to optimiz [...] |
| 16 July 14:20-14:40 (add to calendar) | 519 | Yamil Damian Mahmoud | Integrative transcriptomic analysis and predictive modeling for immunotherapy response in melanoma | TransMed | Despite significant advances in immunotherapies, a substantial subset of melanoma patients remains unresponsive, emphasizing the critical need for pre [...] |
| 16 July 14:20-14:40 (add to calendar) | 519 | Rawan Shraim | A computational approach for the high-throughput identification of cancer-specific antigens for immunotherapeutic development | TransMed | Cancer remains a major global health challenge, with current treatments such as chemotherapy and radiotherapy often limited by toxicity and late effec [...] |
| 16 July 14:25-14:55 (add to calendar) | 520b | Alper Yurtseven | The Antimicrobial Resistance Prediction Challenge | CAMDA | Antimicrobial Resistance (AMR) is an urgent threat to human health worldwide as microbes have developed resistance to even the most advanced drugs. In [...] |
| 16 July 14:40-15:00 (add to calendar) | 520a | Yunzhuo Zhou | DDMut-PPI: predicting effects of mutations on protein-protein interactions using graph-based deep learning | 3DSIG | Protein-protein interactions (PPIs) play a vital role in cellular functions and are essential for therapeutic development and understanding diseases. [...] |
| 16 July 14:40-15:40 (add to calendar) | 524ab | Open Approaches to AI/ML in Bioinformatics | BOSC | ||
| 16 July 14:40-15:00 (add to calendar) | 522 | Joseph Ng | sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data | Computational and Systems Immunology | Class-switch recombination (CSR) is an integral part of B cell maturation. Whilst tools such as pseudotime and RNA velocity exists to infer cellular d [...] |
| 16 July 14:40-15:20 (add to calendar) | 520c | Current and future challenges of Digital Agriculture | Digital Agriculture | ||
| 16 July 14:40-15:00 (add to calendar) | 518 | Semih Kurt | Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix | EvolCompGen | Phylogenetic reconstruction is a fundamental problem in computational biology. The Neighbor Joining (NJ) algorithm offers an efficient distance-based [...] |
| 16 July 14:40-14:50 (add to calendar) | 525 | Ragothaman Yennamalli | Structural Systems Biology of Levan Biosynthesis in Bacillus subtilis | SysMod | Bacillus subtilis is a key organism in biotechnology, with its metabolic capabilities offering potential for various valuable products like levan. Lev [...] |
| 16 July 14:40-15:00 (add to calendar) | 519 | Shi Pan | Leveraging a Single-Cell Language Model for Precise EMT Status Prediction and Gene Signature Identification in Cancer | TransMed | The epithelial-to-mesenchymal transition (EMT) is pivotal in tumour progression and resistance to treatment, yet its heterogeneity complicates the pre [...] |
| 16 July 14:40-15:00 (add to calendar) | 519 | Mozhgan Saeidi | Streamlining Clinical Trial Matching Using a Two-Stage Zero-Shot LLM with Advanced Prompting | TransMed | Identifying patients eligible for clinical trials is a critical bottleneck hindering medical research progress because many clinical trials allow only [...] |
| 16 July 14:50-15:30 (add to calendar) | 525 | Melissa Kemp | Simple rules of intercellular communication for modeling emergent multicellular organization | SysMod | Engineering multicellular systems is enhanced by understanding how collective organization arises during developmental processes through mechanical, b [...] |
| 16 July 14:55-15:15 (add to calendar) | 520b | Jaime Salvador López Viveros | Machine learning models for AMR prediction | CAMDA | Each year, the Community of Interest Critical Assessment of Massive Data Analysis (CAMDA) presents various challenges related to massive data analysis [...] |
| 16 July 15:00-15:20 (add to calendar) | 520a | Qichang Zhao | DDAffinity: Predicting the changes in binding affinity of multiple point mutations using protein three-dimensional structure | 3DSIG | Motivation: Mutations are the crucial driving force for biological evolution as they can disrupt protein stability and protein-protein interactions wh [...] |
| 16 July 15:00-15:20 (add to calendar) | 522 | Lingyu Li | FineST: Super resolved ligand-receptor interaction discovery by fusing spatial RNA-seq and histology images | Computational and Systems Immunology | Cell-cell communication (CCC) is crucial for understanding complex tumor microenvironments, such as interactions between tumor and immune cells. Many [...] |
| 16 July 15:00-15:20 (add to calendar) | 518 | Lars Arvestad | Scalable distance-based phylogeny inference using divide-and-conquer | EvolCompGen | Distance-based methods for inferring evolutionary trees are important subroutines in computational biology, sometimes as a first step in a statistical [...] |
| 16 July 15:00-15:20 (add to calendar) | 519 | Roberto Bonelli | Multi-Omics Integration with High-Resolution AI-Derived Retinal Thickness: Unraveling Spatial Patterns of Retinal Susceptibility to Systemic Influences | TransMed | Retinal thickness is a marker of retinal health and more broadly, a promising biomarker for many systemic diseases. We processed the UK Biobank retina [...] |
| 16 July 15:10-15:30 (add to calendar) | 517d | Alexander Immer | Probabilistic Pathway-based Multimodal Factor Analysis | MLCSB | Multimodal profiling strategies promise to produce more informative insights into biomedical cohorts via the integration of the information each modal [...] |
| 16 July 15:15-15:35 (add to calendar) | 520b | Dexiong Chen | Biomarker identification by interpretable Maximum Mean Discrepancy | CAMDA | Motivation:In many biomedical applications, we are confronted with paired groups of samples, such as treated vs. control. The aim is to detect discri [...] |
| 16 July 15:20-15:40 (add to calendar) | 520a | Yingying Zhang | A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology | 3DSIG | A major goal of cancer biology is to understand the mechanisms underlying tumorigenesis driven by somatically acquired mutations. Two distinct types o [...] |
| 16 July 15:20-15:40 (add to calendar) | 522 | Chang Lu | Computational integration of cellular circuits and immune repertoires based on multilayer network community association | Computational and Systems Immunology | Understanding the role of adaptive immune cells (i.e. T and B lymphocytes) in the immune system is key to treating a range of diseases from autoimmune [...] |
| 16 July 15:20-15:40 (add to calendar) | 520c | Kush Narang | HaloClass: State-of-the-art salt tolerant protein classification with natural language models | Digital Agriculture | Across the globe, increasing soil salinity poses a unique and dangerous threat to food supplies. Past work has suggested that modifying critical enzym [...] |
| 16 July 15:20-16:00 (add to calendar) | 518 | Panel session | EvolCompGen | ||
| 16 July 15:20-15:40 (add to calendar) | 519 | Rachel Melamed | New methods to discover drug combinations impacting cancer incidence | TransMed | In this work we seek to mine health claims data to find combinations of drugs that may alter onset of cancer. This work has an ultimate goal of preven [...] |
| 16 July 15:20-15:40 (add to calendar) | 519 | Closing Remarks | TransMed | ||
| 16 July 15:30-15:40 (add to calendar) | 517d | Jishnu Das | SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains | MLCSB | Modern multi-omic technologies can generate deep multi-scale profiles. However, differences in data modalities, multicollinearity, and large numbers o [...] |
| 16 July 15:30-15:40 (add to calendar) | 525 | Closing Words | SysMod | ||
| 16 July 15:35-15:45 (add to calendar) | 520b | CAMDA Trophy ceremony | CAMDA | ||
| 16 July 15:40-15:40 (add to calendar) | 520c | Final remarks | Digital Agriculture | ||
| 16 July 15:45-15:50 (add to calendar) | 520b | CAMDA summary and closing remarks | CAMDA | ||
| 16 July 16:00-17:00 (add to calendar) | 517d | Su-In Lee | Explainable AI for health: where we are and how to move forward | Distinguished Keynotes | The first part of my talk delves into various research endeavors conducted by my lab, focusing on explainable AI's application across diverse biomedic [...] |